diff --git a/tools.md b/tools.md
index cbd734f58..a69f51787 100644
--- a/tools.md
+++ b/tools.md
@@ -2,15 +2,11 @@
 layout: default
 ---
 
-# European Galaxy tools (3773 and counting)
+# European Galaxy tools (3886 and counting)
 <hr/>
 <h3 id="getdata">Get Data</h3>
-<a href="https://usegalaxy.eu/root?tool_id=diced_database" title="DICED is a web interface for access to proteolytic peptides"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">DICED Database</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=fastq_dl" title="Download FASTQ files from ENA"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">fastq-dl</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=datasets_download_gene" title="download gene sequences and metadata"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NCBI Datasets Gene</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=datasets_download_genome" title="download genome sequence, annotation and metadata"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NCBI Datasets Genomes</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=copernicusmarine" title="retrieve marine data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Copernicus Marine Data Store</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=get_sequences" title="using REST API"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Get sequences by Ensembl ID</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=iedb_api" title="MHC Binding prediction"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">IEDB</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=dbbuilder" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Protein Database Downloader</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=fasterq_dump" title="format from NCBI SRA"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Faster Download and Extract Reads in FASTQ</button></a>
@@ -28,7 +24,7 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=ncbi_eutils_einfo" title="fetch NCBI database metadata"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NCBI EInfo</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ncbi_eutils_esummary" title="fetch summary of history/ids"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NCBI ESummary</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ncbi_eutils_efetch" title="fetch records from NCBI"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NCBI EFetch</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=uniprot" title="ID mapping and retrieval"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">UniProt</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=get_sequences" title="using REST API"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Get sequences by Ensembl ID</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=get_genetree" title="using REST API"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Get gene tree by Ensembl ID</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=get_feature_info" title="using REST API"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Get features by Ensembl ID</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=enasearch_search_data" title="given a query"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Search ENA data</button></a>
@@ -40,20 +36,25 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=dorina_search" title="DoRiNA data source"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">DoRiNA Search</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ebi_metagenomics_run_downloader" title="from EBI Metagenomics database"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Download run data</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=pyega3" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">EGA Download Client</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=WormsMeasurements" title="Enrich dataset with measurement type data from WoRMS"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Enrich dataset with WoRMS</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=openalex_explorer" title="Fetch citing papers from OpenAlex using DOI, openAlex ID, or title"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">OpenAlex explorer</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=diced_database" title="DICED is a web interface for access to proteolytic peptides"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">DICED Database</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=upload1" title="from your computer"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Upload File</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ds_seek_test" title="Trying to get open files out of SEEK"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SEEK test</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=pysradb_search" title="sequence metadata from SRA/ENA"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">pysradb search</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=iabiodiv_smartbiodiv_med_environ" title="From Copernicus and etopo given geolocalized and timestamped observations"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Adds environment variables</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=fastq_dump" title="format from NCBI SRA"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Download and Extract Reads in FASTQ</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=query_impc" title="query tool"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">IMPC</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=mavedb_importer" title="import MAVE data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MaveDB</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=argo_getdata" title="for global ocean in situ observing system"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Argo data access</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=obis_data" title="retrieve data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">OBIS occurences</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=iabiodiv_smartbiodiv_med_environ" title="From Copernicus and etopo given geolocalized and timestamped observations"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Adds environment variables</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=aquainfra_importer" title="downloads content via the AquaINFRA interaction platform"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">AquaINFRA Importer</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=sdmpredictors_list_layers" title="from environmental predictors for species distribution modeling"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SdmPredictors List Layers</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=retrieve_bold" title="Functions to search in Bold and download the available sequences of each subtaxa (get_fasta)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Retrieve bold</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=copernicusmarine" title="retrieve marine data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Copernicus Marine Data Store</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=fastq_dl" title="Download FASTQ files from ENA"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">fastq-dl</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=WormsMeasurements" title="Enrich dataset with measurement type data from WoRMS"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Enrich dataset with WoRMS</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=openalex_explorer" title="Fetch citing papers from OpenAlex using DOI, openAlex ID, or title"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">OpenAlex explorer</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=xarray_import_data" title="Import a dataset from an OPeNDAP URL and convert it to a local NetCDF file using xarray."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Xarray Import Data</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=nfdi4earth_os4a" title="downloads content via NFDI4Earth's OneStop4All search user interface"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NFDI4Earth OneStop4All Importer</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ds_seek_test" title="Trying to get open files out of SEEK"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SEEK test</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ucsc_table_direct1" title="table browser"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">UCSC Main</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ucsc_table_direct_archaea1" title="table browser"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">UCSC Archaea</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ncbi_datasets_source" title="import data from the NCBI Datasets Genomes page"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NCBI Datasets Genomes</button></a>
@@ -82,13 +83,12 @@ layout: default
 <h3 id="senddata">Send Data</h3>
 <a href="https://usegalaxy.eu/root?tool_id=ena_upload" title="Submission of (meta)data to the European Nucleotide Archive (ENA)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ENA Upload tool</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=curl_post" title="send cURL POST requests"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">cURL</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ena_webin_cli" title="Submission of consensus sequences to the European Nucleotide Archive (ENA)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ENA Webin CLI</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=export_remote" title="to repositories"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Export datasets</button></a>
 <h3 id="collectionoperations">Collection Operations</h3>
 <a href="https://usegalaxy.eu/root?tool_id=tp_split_on_column" title="according to the values of a column"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Split file</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=split_file_to_collection" title="to dataset collection"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Split file</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=collapse_dataset" title="into single dataset in order of the collection"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Collapse Collection</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=__FILTER_NULL__" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Filter null elements</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=__KEEP_SUCCESS_DATASETS__" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Keep success</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=unzip" title="Unzip a file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Unzip</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=collection_element_identifiers" title="of a list collection"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Extract element identifiers</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=collection_column_join" title="on multiple datasets"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Column join</button></a>
@@ -97,7 +97,10 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=__ZIP_COLLECTION__" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Zip collections</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=__FILTER_FAILED_DATASETS__" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Filter failed datasets</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=__FILTER_EMPTY_DATASETS__" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Filter empty datasets</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=__FILTER_NULL__" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Filter null elements</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=__KEEP_SUCCESS_DATASETS__" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Keep success</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=__FLATTEN__" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Flatten collection</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=__NEST__" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Nest collection</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=__MERGE_COLLECTION__" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Merge collections</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=__RELABEL_FROM_FILE__" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Relabel identifiers</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=__FILTER_FROM_FILE__" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Filter collection</button></a>
@@ -108,6 +111,7 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=__TAG_FROM_FILE__" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Tag elements</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=__APPLY_RULES__" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Apply rules</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=__BUILD_LIST__" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Build list</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=__SAMPLE_SHEET_TO_TABULAR__" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Sample sheet to tabular</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=__EXTRACT_DATASET__" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Extract dataset</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=__DUPLICATE_FILE_TO_COLLECTION__" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Duplicate file to collection</button></a>
 <h3 id="expressiontools">Expression Tools</h3>
@@ -117,29 +121,9 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=param_value_from_file" title="from dataset"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Parse parameter value</button></a>
 <hr/><h2 id="generaltexttools">General Text Tools</h2>
 <h3 id="textmanipulation">Text Manipulation</h3>
-<a href="https://usegalaxy.eu/root?tool_id=diff" title="analyzes two files and generates an unidiff text file with information about the differences and an optional Html report"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">diff</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=tp_awk_tool" title="with awk"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Text reformatting</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=tp_cat" title="tail-to-head (cat)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Concatenate datasets</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=tp_cut_tool" title="columns from a table (cut)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Advanced Cut</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=tp_easyjoin_tool" title="two files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Join</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=tp_find_and_replace" title="parts of text"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Replace</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=tp_grep_tool" title="(grep)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Search in textfiles</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=tp_head_tool" title="lines from a dataset (head)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Select first</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=tp_multijoin_tool" title="(combine multiple files)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Multi-Join</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=nl" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Number lines</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=tp_text_file_with_recurring_lines" title="with recurring lines"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Create text file</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=tp_replace_in_column" title="in a specific column"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Replace Text</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=tp_replace_in_line" title="in entire line"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Replace Text</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=tp_sed_tool" title="with sed"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Text transformation</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=tp_sort_header_tool" title="data in ascending or descending order"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Sort</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=tp_sort_rows" title="according to their columns"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Sort a row</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=tp_uniq_tool" title="assuming sorted input file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Unique lines</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=tp_tac" title="reverse a file (reverse cat)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">tac</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=tp_tail_tool" title="lines from a dataset (tail)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Select last</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=tp_unfold_column_tool" title="columns from a table"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Unfold</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=tp_sorted_uniq" title="occurrences of each record"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Unique</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=histogram_rpy" title="of a numeric column"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Histogram</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=Add_a_column1" title="on rows"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Compute</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=diff" title="analyzes two files and generates an unidiff text file with information about the differences and an optional Html report"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">diff</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=replace_column_with_key_value_file" title="by values which are defined in a convert file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Replace column</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=add_line_to_file" title="writes a line of text at the begining or end of a text file."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Add line to file</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=addName" title="to an existing tabular file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Add input name as column</button></a>
@@ -149,32 +133,49 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=regexColumn1" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Column Regex Find And Replace</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=regex1" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Regex Find And Replace</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=join_files_on_column_fuzzy" title="on column allowing a small difference"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Join two files</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=tp_find_and_replace" title="parts of text"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Replace</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=query_tabular" title="using sqlite sql"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Query Tabular</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=replace_chromosome_names" title="in a tabular dataset using a mapping table"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Replace chromosome names</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=sqlite_to_tabular" title="for SQL query"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SQLite to tabular</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=tp_replace_in_line" title="in entire line"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Replace Text</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=filter_tabular" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Filter Tabular</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=jq" title="process JSON"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">JQ</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=cast" title="expand combinations of variables:values to columnar format"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">cast</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=tp_replace_in_column" title="in a specific column"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Replace Text</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=melt" title="collapse combinations of variables:values to single lines"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">melt</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=gff3.rebase" title="against parent features"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Rebase GFF3 features</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=gops_cluster_1" title="the intervals of a dataset"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Cluster</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=tp_awk_tool" title="with awk"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Text reformatting</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=column_remove_by_header" title="by heading"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Remove columns</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=column_order_header_sort" title="by heading"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Sort Column Order</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=gops_coverage_1" title="of a set of intervals on second set of intervals"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Coverage</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=tp_tac" title="reverse a file (reverse cat)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">tac</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=tp_cut_tool" title="columns from a table (cut)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Advanced Cut</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=tp_easyjoin_tool" title="two files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Join</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=tp_cat" title="tail-to-head (cat)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Concatenate datasets</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=tp_multijoin_tool" title="(combine multiple files)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Multi-Join</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=tp_uniq_tool" title="assuming sorted input file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Unique lines</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=tp_tail_tool" title="lines from a dataset (tail)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Select last</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=tp_sort_rows" title="according to their columns"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Sort a row</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=tp_sort_header_tool" title="data in ascending or descending order"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Sort</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=tp_grep_tool" title="(grep)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Search in textfiles</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=tp_unfold_column_tool" title="columns from a table"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Unfold</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=tp_sed_tool" title="with sed"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Text transformation</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=tp_text_file_with_recurring_lines" title="with recurring lines"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Create text file</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=tp_head_tool" title="lines from a dataset (head)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Select first</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=tp_sorted_uniq" title="occurrences of each record"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Unique</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=regex_replace" title="Regular Expression replacement using the Python re module"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Regex Replace</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=tables_arithmetic_operations" title="on tables"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Arithmetic Operations</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=gops_merge_1" title="the overlapping intervals of a dataset"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Merge</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=gops_intersect_1" title="the intervals of two datasets"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Intersect</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=gops_coverage_1" title="of a set of intervals on second set of intervals"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Coverage</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=flanking_features_1" title="for every interval"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Fetch closest non-overlapping feature</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=get_flanks1" title="returns flanking region/s for every gene"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Get flanks</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=subtract_query1" title="from another dataset"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Subtract Whole Dataset</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=bg_uniq" title="occurrences of each record"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Unique</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=addValue" title="to an existing dataset"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Add column</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=tp_split_on_column" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Split by group</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=cat_multi_datasets" title="tail-to-head while specifying how"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Concatenate multiple datasets</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=xlsx2tsv" title="with pandas"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Excel to Tabular</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=addValue" title="to an existing dataset"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Add column</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=cat1" title="tail-to-head"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Concatenate datasets</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cat1" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Concatenate multiple datasets or collections</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=Cut1" title="columns from a table"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Cut</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=Convert characters1" title="delimiters to TAB"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=createInterval" title="as a new dataset"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Create single interval</button></a>
@@ -187,16 +188,19 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=trimmer" title="leading or trailing characters"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Trim</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=wc_gnu" title="of a dataset"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Line/Word/Character count</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=secure_hash_message_digest" title="on a dataset"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Secure Hash / Message Digest</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=nl" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Number lines</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=xlsx2tsv" title="with pandas"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Excel to Tabular</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=dos2unix" title="Convert text files with DOS or Mac line breaks to Unix line breaks and other text cleaning options."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Text file format converters (dos2unix)</button></a>
 <h3 id="convertformats">Convert Formats</h3>
-<a href="https://usegalaxy.eu/root?tool_id=geopandas_table2geojson" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Table to GeoJSON</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=markitdown" title="Convert documents to Markdown"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Markitdown</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=10x_bamtofastq" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert a 10X BAM file to FASTQ</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=glimmer_glimmer_to_gff" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert Glimmer to GFF</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=agat" title="GTF/GFF analysis toolkit"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">AGAT</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ucsc_wigtobigwig" title="bedGraph or Wig to bigWig converter"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">wigtobigwig</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=bbgtobigwig" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BAM BED GFF coverage bigWigs</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=uniprot" title="ID mapping and retrieval"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">UniProt</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=markitdown" title="Convert documents to Markdown"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Markitdown</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ffmpeg_converter" title="Convert between video and audio formats using FFmpeg"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FFmpeg Format Converter</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=geopandas_table2geojson" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Table to GeoJSON</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=graphicsmagick_image_convert" title="with GraphicsMagick"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert image format</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=bed2gff1" title="converter"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BED-to-GFF</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=gff2bed1" title="converter"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GFF-to-BED</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=MAF_To_BED1" title="Converts a MAF formatted file to the BED format"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MAF to BED</button></a>
@@ -211,8 +215,8 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=seq_filter_by_id" title="from a tabular file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Filter sequences by ID</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=sample_seqs" title="e.g. to reduce coverage"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Sub-sample sequences files</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=find_in_reference" title="filter peptides that are present in proteins"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">find in reference</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=gffcompare" title="Compare assembled transcripts to a reference annotation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GffCompare</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=bigwig_outlier_bed" title="Writes high and low bigwig runs as features in a bed file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Bigwig outliers to bed features</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=gffcompare" title="compare assembled transcripts to a reference annotation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GffCompare</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=Filter1" title="data on any column using simple expressions"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Filter</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=Grep1" title="lines that match an expression"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Select</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=Grep1" title="lines that match an expression"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Select</button></a>
@@ -232,10 +236,6 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=Grouping1" title="data by a column and perform aggregate operation on other columns."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Group</button></a>
 <hr/><h2 id="genomicfilemanipulation">Genomic File Manipulation</h2>
 <h3 id="convertformats">Convert Formats</h3>
-<a href="https://usegalaxy.eu/root?tool_id=ucsc-twobittofa" title="Convert all or part of .2bit file to FASTA"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">twoBitToFa</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bam2fastx" title="PacBio BAM to Fastx"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PacBio bam2fastx</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=hictk" title="convert cool to juicebox hic"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hictk</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=glimmer_glimmer_to_gff" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert Glimmer to GFF</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=tab2fasta" title="converts tabular file to FASTA format"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Tabular-to-FASTA</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=fasta2tab" title="converter"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FASTA-to-Tabular</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=tabular_to_fastq" title="converter"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Tabular to FASTQ</button></a>
@@ -265,6 +265,8 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=galaxy_intermine_exchange" title="Dataset"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Create InterMine Interchange</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=idconvert" title="Convert mass spectrometry identification files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">idconvert</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=gtftobed12" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert GTF to BED12</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=uniprot" title="ID mapping and retrieval"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">UniProt</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ucsc-twobittofa" title="Convert all or part of .2bit file to FASTA"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">twoBitToFa</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=idpquery" title="Creates text reports from idpDB files."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">idpQuery</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=bam_to_scidx" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert BAM to ScIdx</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=bigwig_to_bedgraph" title="Convert from bigWig to bedGraph format"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bigWigToBedGraph</button></a>
@@ -272,11 +274,6 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=crossmap_region" title="Convert genome coordinates or annotation files between genome assemblies"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CrossMap region</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=samtools_bam_to_cram" title="convert BAM alignments to CRAM format"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">samtools BAM to CRAM</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ab1_fastq_converter" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ab1 to FASTQ converter</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ucsc_chainantirepeat" title="Remove repeated chains"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">chainAntiRepeat</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=tooldistillator" title="Extract information from output files of specific tools and expose it as JSON files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ToolDistillator</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=tooldistillator_summarize" title="Aggregate several JSON reports from ToolDistillator"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ToolDistillator Summarize</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=graphicsmagick_image_compare" title="with GraphicsMagick"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Compare two images</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ucsc_wigtobigwig" title="bedGraph or Wig to bigWig converter"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">wigtobigwig</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=compress_file" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Compress file(s)</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=xmlstarlet" title="convert a metadata XML file in one standard to another"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">xmlstarlet</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=edu.tamu.cpt2.util.mga_to_gff3" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MGA to GFF3</button></a>
@@ -285,16 +282,27 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=edu.tamu.cpt.gff.gff2gb" title="convert gff3 to GenBank"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GFF3 to GenBank</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=edu.tamu.cpt2.gff3.splitGff" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Split GFF3+Fasta into separate parts</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=edu.tamu.cpt.gff3.customGbkToGff" title="CPT made Biobython-based solution"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">(CPT) Genbank to GFF3: </button></a>
+<a href="https://usegalaxy.eu/root?tool_id=graphicsmagick_image_compare" title="with GraphicsMagick"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Compare two images</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=hictk" title="convert cool to juicebox hic"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hictk</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bam2fastx" title="PacBio BAM to Fastx"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PacBio bam2fastx</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=biom_add_metadata" title="to a BIOM table"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Add metadata</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=biom_normalize_table" title="a BIOM table"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Normalize</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=biom_subset_table" title="a BIOM table"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Subset</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=biom_summarize_table" title="in a BIOM table"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Summarize sample or observation data</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=biom_from_uc" title="from a vsearch/uclust/usearch BIOM file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Create a BIOM table</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=tooldistillator" title="Extract information from output files of specific tools and expose it as JSON files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ToolDistillator</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=tooldistillator_summarize" title="Aggregate several JSON reports from ToolDistillator"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ToolDistillator Summarize</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=geopandas_table2geojson" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Table to GeoJSON</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=maftoaxt" title="Convert file from MAF to axt format"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">mafToAxt</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ucsc_axtchain" title="Chain together axt alignments"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">axtChain</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ucsc_nettoaxt" title="Convert net (and chain) to axt format"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">netToAxt</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ucsc_netfilter" title="Filter out parts of net"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">netFilter</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ucsc_chainnet" title="make alignment nets out of alignment chains"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">chainNet</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ucsc_wigtobigwig" title="bedGraph or Wig to bigWig converter"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">wigtobigwig</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=glimmer_glimmer_to_gff" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert Glimmer to GFF</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ucsc_chainantirepeat" title="Remove repeated chains"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">chainAntiRepeat</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=markitdown" title="Convert documents to Markdown"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Markitdown</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ffmpeg_converter" title="Convert between video and audio formats"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FFmpeg Format Converter</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=axt_to_concat_fasta" title="Converts an AXT formatted file to a concatenated FASTA alignment"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">AXT to concatenated FASTA</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=axt_to_fasta" title="Converts an AXT formatted file to FASTA format"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">AXT to FASTA</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=axt_to_lav_1" title="Converts an AXT formatted file to LAV format"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">AXT to LAV</button></a>
@@ -310,105 +318,77 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=bed_to_bigBed" title="converter"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BED-to-bigBed</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=liftOver1" title="between assemblies and genomes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert genome coordinates</button></a>
 <h3 id="fasta/fastq">FASTA/FASTQ</h3>
-<a href="https://usegalaxy.eu/root?tool_id=fastplong" title="Filter and trim long reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Fastplong</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=fastp" title="fast all-in-one preprocessing for FASTQ files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">fastp</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=seqkit_head" title="Displays N records of a FASTA or FASTQ file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SeqKit Head</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bbtools_bbduk" title="decontamination using kmers"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BBTools: BBduk</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bbtools_bbnorm" title="Normalise sequencing coverage"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BBTools: BBNorm</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=fastqc" title="Read Quality reports"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FastQC</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=trim_galore" title="Quality and adapter trimmer of reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Trim Galore!</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=filtlong" title="Filtering long reads by quality"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">filtlong</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=trim_reads" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Select high quality segments</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=cutadapt" title="Remove adapter sequences from FASTQ/FASTA"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Cutadapt</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=fasta-stats" title="display summary statistics for a FASTA file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Fasta Statistics</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=fastqe" title="visualize fastq files with emoji's 🧬😎"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FASTQE</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=rcorrector" title="a kmer-based error correction method for RNA-seq data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RNA-seq Rcorrector</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=umi_tools_count" title="performs quantification of UMIs from BAM files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">UMI-tools count</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=umi_tools_dedup" title="Extract UMI from fastq files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">UMI-tools deduplicate</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=umi_tools_extract" title="Extract UMI from fastq files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">UMI-tools extract</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=umi_tools_group" title="Extract UMI from fastq files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">UMI-tools group</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=umi_tools_whitelist" title="Extract cell barcodes from FASTQ files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">UMI-tools whitelist</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=fasplit" title="Split a FASTA file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">faSplit</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=fastq_paired_end_splitter" title="on joined paired end reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FASTQ splitter</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=seq_filter_by_mapping" title="from SAM/BAM file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Filter sequences by mapping</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=iuc_pear" title="Paired-End read merger"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Pear</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=seqcomplexity" title="total and per read"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Calculate sequence complexity</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=seqkit_stats" title="of FASTA/Q files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SeqKit statistics</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=seqkit_fx2tab" title="convert FASTA/Q to tabular"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SeqKit fx2tab</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=gfastats" title="The swiss army knife for Genome Assembly"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">gfastats</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=adapter_removal" title="from HTS data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">AdapterRemoval: remove adapter sequences</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=seqkit_locate" title="subsequences/motifs, mismatch allowed"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SeqKit locate</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=fasta_regex_finder" title="Search in fasta for regexp match"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Fasta regular expression finder</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=cshl_fastq_quality_boxplot" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Draw quality score boxplot</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bbtools_bbmerge" title="Merge overlapping mates of a read pair"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BBTools: BBMerge</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=cshl_fasta_formatter" title="formatter"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FASTA Width</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=cshl_fasta_nucleotides_changer" title="converter"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RNA/DNA</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=cshl_fastq_quality_converter" title="(ASCII-Numeric)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Quality format converter</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=cshl_fastq_quality_filter" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Filter by quality</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=cshl_fastq_to_fasta" title="converter from FASTX-toolkit"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FASTQ to FASTA</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=cshl_fastx_artifacts_filter" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Remove sequencing artifacts</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=cshl_fastx_barcode_splitter" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Barcode Splitter</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=cshl_fastx_clipper" title="adapter sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Clip</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=cshl_fastx_collapser" title="sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Collapse</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=cshl_fastx_nucleotides_distribution" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Draw nucleotides distribution chart</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=cshl_fastx_quality_statistics" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Compute quality statistics</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=cshl_fastx_renamer" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Rename sequences</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=cshl_fastx_reverse_complement" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Reverse-Complement</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=cshl_fastx_trimmer" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Trim sequences</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=edu.tamu.cpt.fasta.remove_desc" title="from fasta file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Remove Description</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=trimmomatic" title="flexible read trimming tool for Illumina NGS data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Trimmomatic</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=seqtk_comp" title="get the nucleotide composition of FASTA/Q"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">seqtk_comp</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=seqtk_cutN" title="cut sequence at long N"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">seqtk_cutN</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=seqtk_dropse" title="drop unpaired from interleaved Paired End FASTA/Q"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">seqtk_dropse</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=seqtk_fqchk" title="fastq QC (base/quality summary)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">seqtk_fqchk</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=seqtk_hety" title="regional heterozygosity"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">seqtk_hety</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=seqtk_listhet" title="extract the position of each het"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">seqtk_listhet</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=seqtk_mergefa" title="Merge two FASTA/Q files into a FASTA file output"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">seqtk_mergefa</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=seqtk_mergepe" title="interleave two unpaired FASTA/Q files for a paired-end file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">seqtk_mergepe</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=seqtk_mutfa" title="point mutate FASTA at specified positions"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">seqtk_mutfa</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=seqtk_randbase" title="choose a random base from hets"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">seqtk_randbase</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=seqtk_sample" title="random subsample of fasta or fastq sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">seqtk_sample</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=seqtk_seq" title="common transformation of FASTA/Q"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">seqtk_seq</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=seqtk_subseq" title="extract subsequences from FASTA/Q files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">seqtk_subseq</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=seqtk_telo" title="find telomeres"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">seqtk_telo</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=seqtk_trimfq" title="trim FASTQ using the Phred algorithm"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">seqtk_trimfq</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bbtools_tadpole" title="Kmer-based assembler"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BBTools: Tadpole</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=seqprep" title="Merge and Trim Adapter Sequences from Paired-End Illumina Reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Merging paired-end Illumina reads (SeqPrep)</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=rasusa" title="Randomly subsample reads to a specified coverage"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">rasusa</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ncbi_fcs_gx" title="detects contamination from foreign organisms in genome sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NCBI FCS GX</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=art_454" title="simulates pyrosequencing data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ART 454</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=art_illumina" title="simulates sequencing data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ART Illumina</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=art_solid" title="simulates SOLiD data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ART SOLiD</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=falco" title="An alternative, more performant implementation of FastQC for high throughput sequence quality control"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Falco</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=seqkit_translate" title="nucleotid to protein sequence"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SeqKit translate</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=seqkit_sort" title="FASTA or FASTQ files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SeqKit sort</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=cshl_fasta_clipping_histogram" title="chart"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Length Distribution</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=fastq_groomer" title="convert between various FASTQ quality formats"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FASTQ Groomer</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=fastq_combiner" title="into FASTQ"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Combine FASTA and QUAL</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=trim_reads" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Select high quality segments</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=quality_score_distribution" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Build base quality distribution</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=fasta_compute_length" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Compute sequence length</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=fasta_concatenate0" title="FASTA alignment by species"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Concatenate</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=fastq_trimmer" title="by column"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FASTQ Trimmer</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=fastq_quality_trimmer" title="by sliding window"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FASTQ Quality Trimmer</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=fastq_to_fasta_python" title="converter"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FASTQ to FASTA</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=fastq_stats" title="by column"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FASTQ Summary Statistics</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=fastq_to_tabular" title="converter"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FASTQ to Tabular</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=fastq_combiner" title="into FASTQ"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Combine FASTA and QUAL</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=fastq_filter" title="reads by quality score and length"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Filter FASTQ</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=fastq_groomer" title="convert between various FASTQ quality formats"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FASTQ Groomer</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=fastq_manipulation" title="reads on various attributes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Manipulate FASTQ</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=fastq_masker_by_quality" title="by quality score"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FASTQ Masker</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=fastq_paired_end_deinterlacer" title="on paired end reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FASTQ de-interlacer</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=fastq_manipulation" title="reads on various attributes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Manipulate FASTQ</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=fastq_paired_end_joiner" title="on paired end reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FASTQ joiner</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=fastq_paired_end_interlacer" title="on paired end reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FASTQ interlacer</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=fastq_to_tabular" title="converter"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FASTQ to Tabular</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=fastq_trimmer" title="by column"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FASTQ Trimmer</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=fastq_to_fasta_python" title="converter"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FASTQ to FASTA</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=fastq_stats" title="by column"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FASTQ Summary Statistics</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=tabular_to_fastq" title="converter"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Tabular to FASTQ</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=quality_score_distribution" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Build base quality distribution</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=fasta_concatenate0" title="FASTA alignment by species"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Concatenate</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=fastq_quality_trimmer" title="by sliding window"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FASTQ Quality Trimmer</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=sickle" title="Windowed adaptive trimming of FASTQ data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Sickle</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=fastq_paired_end_joiner" title="on paired end reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FASTQ joiner</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=fastq_paired_end_splitter" title="on joined paired end reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FASTQ splitter</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cshl_fastx_renamer" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Rename sequences</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cshl_fastx_reverse_complement" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Reverse-Complement</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cshl_fastx_trimmer" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Trim sequences</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cshl_fastq_to_fasta" title="converter from FASTX-toolkit"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FASTQ to FASTA</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cshl_fastx_quality_statistics" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Compute quality statistics</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cshl_fastq_quality_boxplot" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Draw quality score boxplot</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cshl_fastq_quality_converter" title="(ASCII-Numeric)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Quality format converter</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cshl_fastq_quality_filter" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Filter by quality</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cshl_fasta_formatter" title="formatter"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FASTA Width</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cshl_fasta_nucleotides_changer" title="converter"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RNA/DNA</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=trimmomatic" title="flexible read trimming tool for Illumina NGS data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Trimmomatic</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cshl_fastx_collapser" title="sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Collapse</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=fastqe" title="visualize fastq files with emoji's 🧬😎"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FASTQE</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=fastp" title="fast all-in-one preprocessing for FASTQ files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">fastp</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=fasta_filter_by_length" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Filter sequences by length</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=fasta2tab" title="converter"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FASTA-to-Tabular</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=tabular_to_fastq" title="converter"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Tabular to FASTQ</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=tab2fasta" title="converts tabular file to FASTA format"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Tabular-to-FASTA</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cshl_fastx_artifacts_filter" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Remove sequencing artifacts</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=exonerate" title="pairwise sequence comparison"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Exonerate</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=trim_galore" title="Quality and adapter trimmer of reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Trim Galore!</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=umi_tools_count" title="performs quantification of UMIs from BAM files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">UMI-tools count</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=umi_tools_extract" title="Extract UMI from fastq files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">UMI-tools extract</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=sickle" title="Windowed adaptive trimming of FASTQ data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Sickle</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=seqtk_sample" title="random subsample of fasta or fastq sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">seqtk_sample</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=umi_tools_group" title="Extract UMI from fastq files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">UMI-tools group</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=umi_tools_whitelist" title="Extract cell barcodes from FASTQ files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">UMI-tools whitelist</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=flash" title="adjust length of short reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FLASH</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=seqtk_comp" title="get the nucleotide composition of FASTA/Q"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">seqtk_comp</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=seqtk_mutfa" title="point mutate FASTA at specified positions"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">seqtk_mutfa</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=seqtk_hety" title="regional heterozygosity"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">seqtk_hety</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=seqtk_cutN" title="cut sequence at long N"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">seqtk_cutN</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=seqtk_mergefa" title="Merge two FASTA/Q files into a FASTA file output"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">seqtk_mergefa</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=seqtk_trimfq" title="trim FASTQ using the Phred algorithm"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">seqtk_trimfq</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=seqtk_fqchk" title="fastq QC (base/quality summary)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">seqtk_fqchk</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=seqtk_randbase" title="choose a random base from hets"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">seqtk_randbase</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=seqtk_subseq" title="extract subsequences from FASTA/Q files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">seqtk_subseq</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=seqtk_dropse" title="drop unpaired from interleaved Paired End FASTA/Q"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">seqtk_dropse</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=seqtk_mergepe" title="interleave two unpaired FASTA/Q files for a paired-end file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">seqtk_mergepe</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=seqtk_seq" title="common transformation of FASTA/Q"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">seqtk_seq</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=seqtk_listhet" title="extract the position of each het"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">seqtk_listhet</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=mqc" title="quality control of ribosome profiling mapping results"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">mQC</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=fasta-stats" title="display summary statistics for a FASTA file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Fasta Statistics</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=filtlong" title="Filtering long reads by quality"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">filtlong</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cshl_fastx_clipper" title="adapter sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Clip</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cutadapt" title="Remove adapter sequences from FASTQ/FASTA"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Cutadapt</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cshl_fastx_nucleotides_distribution" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Draw nucleotides distribution chart</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cshl_fastx_barcode_splitter" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Barcode Splitter</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=bctools_extract_crosslinked_nucleotides" title="from full alignments"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Get crosslinked nucleotides</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=fasplit" title="Split a FASTA file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">faSplit</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=atactk_trim_adapters" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Trim putative adapter sequence</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=fastqc" title="Read Quality reports"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FastQC</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=bctools_convert_to_binary_barcode" title="from regular barcodes."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Create binary barcodes</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=bctools_extract_barcodes" title="according to pattern"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Extract barcodes</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=bctools_extract_alignment_ends" title="from SAM or BAM"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Extract alignment ends</button></a>
@@ -419,34 +399,66 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=je_demultiplex" title="demultiplexes fastq files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Je-Demultiplex</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=je_markdupes" title="to filter BAM files for read duplicates taking UMIs into account"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Je-MarkDuplicates</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=je_demultiplex_illu" title="demultiplexes fastq files using Illumina Index file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Je-Demultiplex-Illu</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=umi_tools_dedup" title="Extract UMI from fastq files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">UMI-tools deduplicate</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=fasta_merge_files_and_filter_unique_sequences" title="Concatenate FASTA database files together"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FASTA Merge Files and Filter Unique Sequences</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=align_back_trans" title="Gives a codon aware alignment"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Thread nucleotides onto a protein alignment (back-translation)</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=seq_filter_by_mapping" title="from SAM/BAM file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Filter sequences by mapping</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=prinseq" title="to process quality of sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PRINSEQ</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=lighter" title="can correct the reads containing sequence errors"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">lighter</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=fastq_join" title="- Joins two paired-end reads on the overlapping ends"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">fastq-join</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=rbc_splitfasta" title="files into a collection"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Split Fasta</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=rbc_splitfasta" title="files into a collection"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Split Fasta</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=solid2fastq" title="SOLiD output to fastq"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=solid_qual_stats" title="for SOLiD data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Compute quality statistics</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=solid_qual_boxplot" title="for SOLiD data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Draw quality score boxplot</button></a>
-<h3 id="qualitycontrol">Quality Control</h3>
-<a href="https://usegalaxy.eu/root?tool_id=multiqc" title="aggregate results from bioinformatics analyses into a single report"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MultiQC</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=qualimap_counts" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">QualiMap Counts QC</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=fastq_info" title="validates single or paired fastq files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FASTQ info</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=sequali" title="Fast sequencing data quality metrics for short and long reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">sequali</button></a>
-<h3 id="sam/bam">SAM/BAM</h3>
-<a href="https://usegalaxy.eu/root?tool_id=tasmanian_mismatch" title="Quantify, visualize and summarize mismatches in deep sequencing data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Analysis of artifacts with Tasmanian</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=samtools_slice_bam" title="BAM by genomic regions"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Slice</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=samtools_flagstat" title="tabulate descriptive stats for BAM datset"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Samtools flagstat</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=samtools_coverage" title="Produces a histogram or table of coverage per chromosome"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Samtools coverage</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=sambamba_sort" title="Tool to sort BAM files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Sambamba sort</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=pileup_interval" title="condenses pileup format into ranges of bases"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Pileup-to-Interval</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=pileup_parser" title="on coverage and SNPs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Filter pileup</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bbtools_bbduk" title="decontamination using kmers"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BBTools: BBduk</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=rcorrector" title="a kmer-based error correction method for RNA-seq data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RNA-seq Rcorrector</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=iuc_pear" title="Paired-End read merger"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Pear</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=seqcomplexity" title="total and per read"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Calculate sequence complexity</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=seqkit_stats" title="of FASTA/Q files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SeqKit statistics</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=seqkit_fx2tab" title="convert FASTA/Q to tabular"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SeqKit fx2tab</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=adapter_removal" title="from HTS data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">AdapterRemoval: remove adapter sequences</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=seqkit_locate" title="subsequences/motifs, mismatch allowed"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SeqKit locate</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=fasta_regex_finder" title="Search in fasta for regexp match"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Fasta regular expression finder</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bbtools_bbmerge" title="Merge overlapping mates of a read pair"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BBTools: BBMerge</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=edu.tamu.cpt.fasta.remove_desc" title="from fasta file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Remove Description</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=seqtk_telo" title="find telomeres"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">seqtk_telo</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bbtools_tadpole" title="Kmer-based assembler"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BBTools: Tadpole</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=seqprep" title="Merge and Trim Adapter Sequences from Paired-End Illumina Reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Merging paired-end Illumina reads (SeqPrep)</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=rasusa" title="Randomly subsample reads to a specified coverage"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">rasusa</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ncbi_fcs_gx" title="detects contamination from foreign organisms in genome sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NCBI FCS GX</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=art_454" title="simulates pyrosequencing data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ART 454</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=art_illumina" title="simulates sequencing data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ART Illumina</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=art_solid" title="simulates SOLiD data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ART SOLiD</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=falco" title="An alternative, more performant implementation of FastQC for high throughput sequence quality control"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Falco</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=seqkit_translate" title="nucleotid to protein sequence"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SeqKit translate</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=seqkit_sort" title="FASTA or FASTQ files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SeqKit sort</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cshl_fasta_clipping_histogram" title="chart"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Length Distribution</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cshl_fasta_clipping_histogram" title="chart"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Length Distribution</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=solid2fastq" title="SOLiD output to fastq"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=solid_qual_stats" title="for SOLiD data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Compute quality statistics</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=solid_qual_boxplot" title="for SOLiD data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Draw quality score boxplot</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=seqkit_head" title="Displays N records of a FASTA or FASTQ file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SeqKit Head</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bbtools_bbnorm" title="Normalise sequencing coverage"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BBTools: BBNorm</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=fastplong" title="Filter and trim long reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Fastplong</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cialign" title="clean, visualise and analyse a multiple sequence alignment"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CIAlign</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=rrmscorer" title="Predicts RNA Recognition Motif (RRM) scores"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RRM-Scorer</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=seqkit_split2" title="Split sequences into files by part size, number of parts, or length"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Seqkit Split2</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=rdeval" title="Multithreaded read analysis and manipulation tool."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">rdeval</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=rdeval_report" title="Read summary and figures."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">rdeval report</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=fastq_groupmerge" title="Group FASTQ files together based on a set grouping in a metadata file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Fastq groupmerge</button></a>
+<h3 id="qualitycontrol">Quality Control</h3>
+<a href="https://usegalaxy.eu/root?tool_id=multiqc" title="aggregate results from bioinformatics analyses into a single report"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MultiQC</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qualimap_counts" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">QualiMap Counts QC</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=fastq_info" title="validates single or paired fastq files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FASTQ info</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=sequali" title="Fast sequencing data quality metrics for short and long reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">sequali</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=fileidentification" title="Check multimedia files if they are corrupt or duplicated"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">File Format Identification</button></a>
+<h3 id="sam/bam">SAM/BAM</h3>
+<a href="https://usegalaxy.eu/root?tool_id=pileup_interval" title="condenses pileup format into ranges of bases"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Pileup-to-Interval</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=pileup_parser" title="on coverage and SNPs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Filter pileup</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=sam2interval" title="to interval"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert SAM</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=sam_merge2" title="merges BAM files together"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Merge BAM Files</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=sam_pileup" title="from BAM dataset"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Generate pileup</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=samtools_flagstat" title="tabulate descriptive stats for BAM datset"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Samtools flagstat</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=samtools_mpileup" title="multi-way pileup of variants"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Samtools mpileup</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=samtools_rmdup" title="remove PCR duplicates"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RmDup</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=samtools_slice_bam" title="BAM by genomic regions"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Slice</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=samtools_view" title="- reformat, filter, or subsample SAM, BAM or CRAM"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Samtools view</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=samtools_reheader" title="copy SAM/BAM header between datasets"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Samtools reheader</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=qualimap_bamqc" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">QualiMap BamQC</button></a>
@@ -464,6 +476,7 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=samtools_bedcov" title="calculate read depth for a set of genomic intervals"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Samtools bedcov</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=samtools_depth" title="compute the depth at each position or region"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Samtools depth</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=samtools_sort" title="order of storing aligned sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Samtools sort</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=samtools_coverage" title="Produces a histogram or table of coverage per chromosome"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Samtools coverage</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ngsutils_bam_filter" title="Removes reads from a BAM file based on criteria"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BAM filter</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=bamFilter" title="datasets on a variety of attributes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Filter BAM</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=samtools_calmd" title="recalculate MD/NM tags"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Samtools calmd</button></a>
@@ -473,15 +486,18 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=bamtools_split_ref" title="into a dataset list collection"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Split BAM by reference</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=bamtools_split_mapped" title="into a mapped and an unmapped dataset"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Split BAM by reads mapping status</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=bamtools_split_tag" title="into a dataset list collection"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Split BAM by read tag value</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=sambamba_markdup" title="Finds and marks duplicate reads in BAM files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Sambamba markdup</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=sambamba_merge" title="Merge several BAM files into one"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Sambamba merge</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=samtools_ampliconclip" title="clip primer bases from bam files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Samtools ampliconclip</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=samtools_ampliconclip" title="clip primer bases from bam files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Samtools ampliconclip</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bamtools_split_tag" title="into a dataset list collection"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Split BAM by read tag value</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=bamutil_diff" title="two coordinate sorted SAM/BAM files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BamUtil diff</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=samtools_ampliconclip" title="clip primer bases from bam files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Samtools ampliconclip</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=revertR2orientationInBam" title="Revert the mapped orientation of R2 mates in a bam."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">revertR2orientationInBam</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=bamtools_split" title="BAM datasets on variety of attributes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Split</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=mosdepth" title="- fast and flexible depth coverage calculation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">mosdepth</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=tasmanian_mismatch" title="Quantify, visualize and summarize mismatches in deep sequencing data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Analysis of artifacts with Tasmanian</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=sambamba_flagstat" title="Retrieving flag statistics from BAM file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Sambamba flagstat</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=sambamba_markdup" title="Finds and marks duplicate reads in BAM files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Sambamba markdup</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=sambamba_merge" title="Merge several BAM files into one"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Sambamba merge</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=sambamba_sort" title="Tool to sort BAM files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Sambamba sort</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=samtools_consensus" title="generate consensus from a SAM, BAM or CRAM file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Samtools consensus</button></a>
 <h3 id="bed">BED</h3>
 <a href="https://usegalaxy.eu/root?tool_id=bedtools_expandbed" title="replicate lines based on lists of values in columns"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bedtools ExpandBed</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=bedtools_nucbed" title="profile the nucleotide content of intervals in a FASTA file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bedtools NucBed</button></a>
@@ -522,9 +538,9 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=bedtools_fisher" title="calculate Fisher statistic between two feature files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bedtools FisherBed</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=bedtools_bamtofastq" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bedtools Convert from BAM to FastQ</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=bedtools_genomecoveragebed_bedgraph" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Create a BedGraph of genome coverage</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bedops-sort-bed" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bedops sort-bed</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=bedtools_mergebedgraph" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Merge BedGraph files</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=bedtools_genomecoveragebed_histogram" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Create a histogram of genome coverage</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bedops-sort-bed" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bedops sort-bed</button></a>
 <h3 id="vcf/bcf">VCF/BCF</h3>
 <a href="https://usegalaxy.eu/root?tool_id=vcffilter2" title="filter VCF data in a variety of attributes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VCFfilter:</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=vcfcheck" title="Verify that the reference allele matches the reference genome"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VCFcheck:</button></a>
@@ -560,17 +576,15 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=vcftools_slice" title="to get data from selected regions"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Slice VCF</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=vcftools_subset" title="columns from a VCF dataset"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Subset</button></a>
 <h3 id="nanopore">Nanopore</h3>
-<a href="https://usegalaxy.eu/root?tool_id=clair3" title="germline small variant caller for long-reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Clair3</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=porechop" title="adapter trimmer for Oxford Nanopore reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Porechop</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=nanoplot" title="Plotting suite for Oxford Nanopore sequencing data and alignments"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NanoPlot</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=medaka_variant" title="decodes variant calls from medaka consensus output"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">medaka variant tool</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=medaka_variant" title="decodes variant calls from medaka consensus output"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">medaka vcf tool</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=flair_correct" title="corrects misaligned splice sites using genome annotations"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FLAIR correct</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=flair_collapse" title="defines high-confidence isoforms from flair-corrected reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FLAIR collapse</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ngmlr" title="Gap-cost alignMents for Long Reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CoNvex</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=medaka_variant_pipeline" title="via neural networks"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">medaka variant pipeline</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=medaka_consensus_pipeline" title="Assembly polishing via neural networks"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">medaka consensus pipeline</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=medaka_consensus" title="Assembly polishing via neural networks"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">medaka consensus tool</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=medaka_consensus" title="inference from a trained model and alignments."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">medaka inference tool</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=nanocompore_db" title="Process SampComp results database"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NanoComporeDB</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=nanoplot" title="Plotting suite for Oxford Nanopore sequencing data and alignments"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NanoPlot</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ont_fast5_api_multi_to_single_fast5" title="read file(s)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ont_fast5_api: Multi to single</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ont_fast5_api_single_to_multi_fast5" title="read file(s)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ont_fast5_api: Single to multi</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ont_fast5_api_compress_fast5" title="multi read file(s)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ont_fast5_api: Compress</button></a>
@@ -582,6 +596,7 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=nanocompore_sampcomp" title="to compare Nanopolished datasets"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SampComp</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=nanopolishcomp_freqmethcalculate" title="calculates methylation frequency at genomic CpG sites"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NanopolishComp: FreqMethCalculate</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=nanopolishcomp_eventaligncollapse" title="by kmers rather than by event"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NanopolishComp: EventalignCollapse</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=porechop" title="adapter trimmer for Oxford Nanopore reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Porechop</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=poretools_times" title="and channel information from a set of FAST5 files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Extract time</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=poretools_nucdist" title="distribution in nanopore sequencing reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Show nucleotide</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=poretools_qualdist" title="score distribution in nanopore sequencing reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Show quality</button></a>
@@ -596,19 +611,23 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=poretools_winner" title="from a set of FAST5 files."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Get longest read</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=poretools_events" title="from a set of sequencing reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Extract nanopore events</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=pycoqc" title="quality control for Nanopore sequencing data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Pycoqc</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=clair3" title="germline small variant caller for long-reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Clair3</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=m6anet" title="to detect m6A RNA modifications from nanopore data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">m6anet</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=nanofilt" title="Filtering and trimming of long read sequencing data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NanoFilt</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=nanocomp" title="Compare multiple runs of long read sequencing data and alignments"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NanoComp</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=chopper" title="Filtering and trimming of long reads."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Chopper</button></a>
 <hr/><h2 id="commongenomicstools">Common Genomics Tools</h2>
 <h3 id="operateongenomicintervals">Operate on Genomic Intervals</h3>
-<a href="https://usegalaxy.eu/root?tool_id=translate_bed_sequences" title="3 frame translation of BED augmented with a sequence column"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Translate BED Sequences</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=filter_bed_on_splice_junctions" title="that are not in a reference bed file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Filter BED on splice junctions</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=gops_cluster_1" title="the intervals of a dataset"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Cluster</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=tbl2gff3" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Table to GFF3</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=translate_bed" title="cDNA in 3frames or CDS"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Translate BED transcripts</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=gops_basecoverage_1" title="of all intervals"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Base Coverage</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=gops_complement_1" title="intervals of a dataset"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Complement</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=translate_bed_sequences" title="3 frame translation of BED augmented with a sequence column"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Translate BED Sequences</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=gops_subtract_1" title="the intervals of two datasets"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Subtract</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=gops_concat_1" title="two BED files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Concatenate</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=gops_join_1" title="the intervals of two datasets side-by-side"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Join</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=filter_bed_on_splice_junctions" title="that are not in a reference bed file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Filter BED on splice junctions</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=aggregate_scores_in_intervals2" title="Appends the average, min, max of datapoints per interval"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Aggregate datapoints</button></a>
 <h3 id="fetchsequences/alignments">Fetch Sequences / Alignments</h3>
 <a href="https://usegalaxy.eu/root?tool_id=Extract genomic DNA 1" title="using coordinates from assembled/unassembled genomes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Extract Genomic DNA</button></a>
@@ -630,86 +649,137 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=MAF_filter" title="by specified attributes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Filter MAF</button></a>
 <hr/><h2 id="genomicsanalysis">Genomics Analysis</h2>
 <h3 id="annotation">Annotation</h3>
-<a href="https://usegalaxy.eu/root?tool_id=omark" title="proteome quality assessment"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">OMArk</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=funannotate_sort" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Sort assembly</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=multigsea" title="GSEA-based pathway enrichment analysis for multi-omics data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">multiGSEA</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=deeparg_short_reads" title="pipeline to detect Antibiotic Resistance Genes (ARGs) from raw reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">DeepARG short reads</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=deeparg_predict" title="Antibiotic Resistance Genes (ARGs) from metagenomes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">DeepARG predict</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=sanntis_marine" title="in genomic and metagenomic data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Sanntis biosynthetic gene clusters</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=CryptoGenotyper" title="classifies Cryptosporidium species subtypes based on SSU rRNA and gp60 gene markers from Sanger sequencing data."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CryptoGenotyper</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=coreprofiler_allele_calling" title="Calls cgMLST alleles from a bacterial genome using a reference scheme"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CoreProfiler allele_calling</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=busco" title="Assess genome assembly and annotation completeness"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Busco</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=optitype" title="HLA genotyping predictions from NGS data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">OptiType</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=prokka" title="Prokaryotic genome annotation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Prokka</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=roary" title="the pangenome pipeline - Quickly generate a core gene alignment from gff3 files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Roary</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=tb_profiler_profile" title="Infer strain types and drug resistance markers from sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">TB-Profiler Profile</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=hmmer_nhmmer" title="search a DNA model or alignment against a DNA database (BLASTN-like)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">nhmmer</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=hmmer_hmmbuild" title="Build a profile HMM from an input multiple alignment"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hmmbuild</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=hmmer_hmmscan" title="search protein sequence(s) against a protein profile database"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hmmscan</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=hmmer_phmmer" title="search a protein sequence against a protein database (BLASTP-like)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">phmmer</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=hmmer_jackhmmer" title="iteratively search a protein sequence against a protein database (PSIBLAST-like)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">jackhmmer</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=hmmer_nhmmscan" title="search DNA sequence(s) against a DNA profile database"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">nhmmscan</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=hmmer_hmmsearch" title="search profile(s) against a sequence database"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hmmsearch</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=kofamscan" title="gene function annotation based on KEGG orthology and HMM"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">KofamScan</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=tbl2gff3" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Table to GFF3</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=annotatemyids" title="annotate a generic set of identifiers"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">annotateMyIDs</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=mob_recon" title="Type contigs and extract plasmid sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MOB-Recon</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=mob_typer" title="Get the plasmid type and mobility given its sequence"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MOB-Typer</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ectyper" title="ectyper is a standalone serotyping module for Escherichia coli. It supports fasta and fastq file formats."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ectyper</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=sistr_cmd" title="Salmonella In Silico Typing Resource command-line tool for serovar prediction"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">sistr_cmd</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=mitos" title="de-novo annotation of metazoan mitochondrial genomes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MITOS</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=antismash" title="allows the genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Antismash</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=chipseeker" title="for ChIP peak annotation and visualization"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ChIPseeker</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=progressivemauve" title="constructs multiple genome alignments"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">progressiveMauve</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=xmfa2gff3" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert XMFA to gapped GFF3</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=mlst_list" title="Lists available schemes for the MLST tool"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MLST List</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=mlst" title="Scans genomes against PubMLST schemes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MLST</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bp_genbank2gff3" title="converter"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Genbank to GFF3</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=mitos2" title="de-novo annotation of metazoan mitochondrial genomes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MITOS2</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=exonerate" title="pairwise sequence comparison"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Exonerate</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=seq2hla" title="HLA genotype and expression from RNA-seq"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">seq2HLA</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=fastani" title="fast alignment-free computation of whole-genome Average Nucleotide Identity"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FastANI</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=transit_tn5gaps" title="- determine essential genes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">TRANSIT Tn5Gaps</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=transit_resampling" title="- determine per-gene p-values"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">TRANSIT Resampling</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=transit_hmm" title="- determine essentiality of a genome"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">TRANSIT HMM</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=transit_gumbel" title="- determine essential genes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">TRANSIT Gumbel</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=tetyper" title="Transposable Element Typer"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">TETyper</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=augustus_training" title="ab-initio gene predictor"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Train Augustus</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=augustus" title="gene prediction for prokaryotic and eukaryotic genomes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Augustus</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=snpSift_geneSets" title="Annotating GeneSets, such as Gene Ontology, KEGG, Reactome"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SnpSift GeneSets</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=aragorn_trna" title="prediction (Aragorn)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">tRNA and tmRNA</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=dgidb_annotator" title="database info"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Annotate with DGI</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=fargene" title="Fragmented antibiotic resistance gene identifier"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">fargene</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=kobas_annotate" title="KEGG Orthology Based Annotation System"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">KOBAS Annotate</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=kobas_identify" title="KEGG Orthology Based Annotation System"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">KOBAS Identify</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=gff_to_prot" title="to prot_table for TRANSIT"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert GFF3</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=gprofiler_snpense" title="maps SNP rs-codes to gene names, chromosomal coordinates and variant effects"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">gProfiler SNPense</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=gprofiler_random" title="generates a gene list"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">gProfiler Random</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=gprofiler_gost" title="performs functional enrichment analysis of gene lists"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">gProfiler GOSt</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=gprofiler_orth" title="translates gene identifiers between organisms"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">gProfiler Orth</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=gprofiler_convert" title="converts between various types of namespaces"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">gProfiler Convert</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=abricate" title="Mass screening of contigs for antimicrobial and virulence genes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ABRicate</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=abricate_list" title="List all of abricate's available databases."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ABRicate List</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=blastxml_to_gapped_gff3" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BlastXML to gapped GFF3</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=maker" title="genome annotation pipeline"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Maker</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=Add_a_column1" title="an expression on every row"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Compute</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=socru" title="Calculate the order and orientation of complete bacterial genomes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">socru</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=goseq" title="tests for overrepresented gene categories"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">goseq</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=snap_training" title="ab-initio gene predictor"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Train SNAP</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=maker_map_ids" title="on a Maker annotation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Map annotation ids</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=fgsea" title="- fast preranked gene set enrichment analysis"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">fgsea</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=spaln" title="Maps and aligns a set of cDNA or protein sequences onto a whole genomic sequence."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Spaln: align cDNA or Protein to genome</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=goslimmer" title="converts a set of annotation from GO to a given GOSlim version"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GOSlimmer</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=goenrichment" title="performs GO enrichment analysis of a set of gene products"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GOEnrichment</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=jcvi_gff_stats" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Genome annotation statistics</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=Psortb" title="Determines sub-cellular localisation of bacterial/archaeal protein sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">psortb</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=rxlr_motifs" title="Find RXLR Effectors of Plant Pathogenic Oomycetes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RXLR Motifs</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=signalp3" title="Find signal peptides in protein sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SignalP 3.0</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=promoter2" title="Find eukaryotic PolII promoters in DNA sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Promoter 2.0</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=tmhmm2" title="Find transmembrane domains in protein sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">TMHMM 2.0</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=rxlr_motifs" title="Find RXLR Effectors of Plant Pathogenic Oomycetes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RXLR Motifs</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=wolf_psort" title="Eukaryote protein subcellular localization prediction"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">WoLF PSORT</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=picrust_metagenome_contributions" title="of OTUs to user-specified functions"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Metagenome Contributions</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=picrust_format_tree_and_trait_table" title="tree and trait tables"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Format</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=picrust_compare_biom" title="Compare the accuracy of biom files (expected and observed) either by observations (default) or by samples."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Compare BIOM tables</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=picrust_predict_metagenomes" title="based on the abundance of OTUs and a functional database"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Predict Metagenome</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=picrust_categorize" title="by collapsing hierarchical data to a specified functional level"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Categorize</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=trnascan" title="(tRNAscan)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">tRNA prediction</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=aragorn_trna" title="prediction (Aragorn)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">tRNA and tmRNA</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=transtermhp" title="finds rho-independent transcription terminators in bacterial genomes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">TransTermHP</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=smf_utils_estimate-energy" title="Estimates whether a certain Segment(Loop) is present and for which delta-G this transistion takes place"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">estimate-energy</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=smf_utils_fix-fasta-headers" title="Replaces all spaces with underscores in the '>..'-sequence headers of a FASTA file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">fix-fasta-headers</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=smf_utils_filter-annotated-entries" title="Split entries into two files based on whether they overlap annotations in a bed file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">filter-annotated-entries</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=smf_utils_add-read-counts" title="Annotate sequences by adding the read counts from a bam file, within a region contained in the fasta header of the dbn file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">add-read-counts</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=smf_utils_find-boxes" title="Finds all occurances of two given boxes (sequence motifs) within a FASTA file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">find-boxes</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=smf_utils_filter-by-energy" title="Split entries over two files based on the estimated energy"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">filter-by-energy</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=smf_utils_extract-boxed-sequences" title="Extracts boxed sequences from bed_input_file which has to be created with 'find-box', part of this utility"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">extract-boxed-sequences</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=segmentation_fold" title="RNA-Folding including predefined segments including K-turns"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">segmentation-fold</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=gubbins" title="Recombination detection in Bacteria"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Gubbins</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bg_sortmerna" title="of ribosomal RNAs in metatranscriptomic data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Filter with SortMeRNA</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=Probmetab" title="Wrapper function for ProbMetab R package."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ProbMetab Tool</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=lcmsmatching" title="Annotation of MS peaks using matching on a spectra database."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">LC/MS matching</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=Nucleosome" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Nucleosome Predictions</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=orthofinder_onlygroups" title="finds orthogroups in a set of proteomes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">OrthoFinder</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=miranda" title="finds potential target sites for miRNAs in genomic sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">miRanda</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=dotknot" title="pseudoknot prediction in a given RNA sequence"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">DotKnot</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=hmmer_alimask" title="append modelmask line to a multiple sequence alignments"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">alimask</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=hmmer_hmmalign" title="align sequences to a profile HMM"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hmmalign</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=hmmer_hmmconvert" title="convert profile file to a HMMER format"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hmmconvert</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=hmmer_hmmemit" title="sample sequence(s) from a profile HMM"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hmmemit</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=hmmer_hmmfetch" title="retrieve profile HMM(s) from a file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hmmfetch</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bg_find_subsequences" title="providing regions in BED format"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Nucleotide subsequence search</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=rbc_gotohscan" title="Find subsequences in db"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GotohScan</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=sanntis_marine" title="in genomic and metagenomic data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Sanntis biosynthetic gene clusters</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CryptoGenotyper" title="classifies Cryptosporidium species subtypes based on SSU rRNA and gp60 gene markers from Sanger sequencing data."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CryptoGenotyper</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=dgidb_annotator" title="database info"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Annotate with DGI</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=dgidb_annotate" title="database info"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Annotate with DGI</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=hhsearch" title="detecting remote homologues of proteins"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">HHsearch</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=sistr_cmd" title="Salmonella In Silico Typing Resource command-line tool for serovar prediction"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">sistr_cmd</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=seq2hla" title="HLA genotype and expression from RNA-seq"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">seq2HLA</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=busco" title="Assess genome assembly and annotation completeness"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Busco</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=optitype" title="HLA genotyping predictions from NGS data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">OptiType</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=abricate_summary" title="Combine ABRicate results into a simple matrix of gene presence/absence"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ABRicate Summary</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=tb_profiler_profile" title="Infer strain types and drug resistance markers from sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">TB-Profiler Profile</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=mitos" title="de-novo annotation of metazoan mitochondrial genomes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MITOS</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=mitos2" title="de-novo annotation of metazoan mitochondrial genomes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MITOS2</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=glimmer_build_icm" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Glimmer ICM builder</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=glimmer_knowledge_based" title="Predict ORFs in prokaryotic genomes (knowlegde-based)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Glimmer3</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=glimmer_not_knowledge_based" title="Predict ORFs in prokaryotic genomes (not knowlegde-based)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Glimmer3</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=goseq" title="tests for overrepresented gene categories"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">goseq</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=maker" title="genome annotation pipeline"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Maker</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=tbvcfreport" title="- generate HTML report from SnpEff annotated M.tb VCF(s)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">TB Variant Report</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=tb_variant_filter" title="M. tuberculosis H37Rv VCF filter"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">TB Variant Filter</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=annotatemyids" title="annotate a generic set of identifiers"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">annotateMyIDs</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=augustus_training" title="ab-initio gene predictor"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Train Augustus</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=hmmer_hmmsearch" title="search profile(s) against a sequence database"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hmmsearch</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=hmmer_hmmemit" title="sample sequence(s) from a profile HMM"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hmmemit</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=hmmer_hmmalign" title="align sequences to a profile HMM"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hmmalign</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=hmmer_nhmmscan" title="search DNA sequence(s) against a DNA profile database"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">nhmmscan</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=hmmer_jackhmmer" title="iteratively search a protein sequence against a protein database (PSIBLAST-like)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">jackhmmer</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=hmmer_phmmer" title="search a protein sequence against a protein database (BLASTP-like)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">phmmer</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=hmmer_hmmscan" title="search protein sequence(s) against a protein profile database"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hmmscan</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=hmmer_hmmfetch" title="retrieve profile HMM(s) from a file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hmmfetch</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=hmmer_alimask" title="append modelmask line to a multiple sequence alignments"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">alimask</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=hmmer_hmmconvert" title="convert profile file to a HMMER format"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hmmconvert</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=hmmer_hmmbuild" title="Build a profile HMM from an input multiple alignment"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hmmbuild</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=hmmer_nhmmer" title="search a DNA model or alignment against a DNA database (BLASTN-like)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">nhmmer</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=mob_recon" title="Type contigs and extract plasmid sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MOB-Recon</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=mob_typer" title="Get the plasmid type and mobility given its sequence"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MOB-Typer</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=lorikeet_spoligotype" title="M. tuberculosis DNA fingerprinting"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">lorikeet spoligotyping</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=spotyping" title="fast and accurate in silico Mycobacterium spoligotyping from sequence reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SpoTyping</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=repeatmodeler" title="Model repetitive DNA"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RepeatModeler</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=chipseeker" title="for ChIP peak annotation and visualization"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ChIPseeker</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=repeatmasker_wrapper" title="screen DNA sequences for interspersed repeats and low complexity regions"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RepeatMasker</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=homer_scanMotifGenomeWide" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">scanMotifGenomeWide</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=homer_annotatePeaks" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">annotatePeaks</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=homer_findMotifsGenome" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">findMotifsGenome</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=homer_gtf_to_annotations" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Converts GTF to Annotations file for Homer</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=prokka" title="Prokaryotic genome annotation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Prokka</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=snpSift_geneSets" title="Annotating GeneSets, such as Gene Ontology, KEGG, Reactome"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SnpSift GeneSets</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=hamronize_tool" title="Antimicrobial Resistance Analysis Reports into a common data structure"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hAMRonize</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=hamronize_summarize" title="Concatenate and summarize AMR detection reports"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hamronize summarize:</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=funannotate_clean" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Funannotate assembly clean</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=funannotate_predict" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Funannotate predict annotation</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=funannotate_sort" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Sort assembly</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=funannotate_compare" title="annotations"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Funannotate compare</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=funannotate_annotate" title="annotation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Funannotate functional</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=roary" title="the pangenome pipeline - Quickly generate a core gene alignment from gff3 files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Roary</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=list_spaln_tables" title="Given a query species, list the spaln settings tables that exist, from closest related species to most different"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">List spaln parameter tables</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=spaln" title="Maps and aligns a set of cDNA or protein sequences onto a whole genomic sequence."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Spaln: align cDNA or Protein to genome</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=gecco" title="is a fast and scalable method for identifying putative novel Biosynthetic Gene Clusters (BGCs) in genomic and metagenomic data using Conditional Random Fields (CRFs)."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GECCO</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=interproscan" title="functional annotation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">InterProScan</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=transit_gumbel" title="- determine essential genes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">TRANSIT Gumbel</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=transit_resampling" title="- determine per-gene p-values"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">TRANSIT Resampling</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=transit_tn5gaps" title="- determine essential genes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">TRANSIT Tn5Gaps</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=transit_hmm" title="- determine essentiality of a genome"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">TRANSIT HMM</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=kofamscan" title="gene function annotation based on KEGG orthology and HMM"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">KofamScan</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=legsta" title="Legionella pneumophila sequence based typing"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">legsta</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=signalp3" title="Find signal peptides in protein sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SignalP 3.0</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=wolf_psort" title="Eukaryote protein subcellular localization prediction"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">WoLF PSORT</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=antismash" title="allows the genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Antismash</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=te_finder" title="Transposable element insertions finder"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">TEfinder</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=gubbins" title="Recombination detection in Bacteria"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Gubbins</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=isescan" title="Insertion Sequence Elements detection in prokaryotic genomes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ISEScan</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=miniprot" title="align a protein sequence against a genome with affine gap penalty, splicing and frameshift"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Miniprot align</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=netboxr" title="enables automated discovery of biological process modules by network analysis."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">netboxr</button></a>
@@ -724,9 +794,8 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=pfamscan" title="search a FASTA sequence against a library of Pfam HMM"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PfamScan</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=pharokka" title="Rapid standardised annotation tool for bacteriophage genomes and metagenomes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">pharokka</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=homer_findMotifs" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">findMotifs</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=mlst" title="Scans genomes against PubMLST schemes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MLST</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=mlst_list" title="Lists available schemes for the MLST tool"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MLST List</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=braker" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Braker genome annotation</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=multigsea" title="GSEA-based pathway enrichment analysis for multi-omics data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">multiGSEA</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=get_orfs_or_cdss" title="e.g. to get peptides from ESTs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Get open reading frames (ORFs) or coding sequences (CDSs)</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=edu.tamu.cpt.gff3.cdsParents" title="is one step of fixing a gene model--adding parent gene features to CDSs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GFF3 Add Gene to CDS</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=edu.tamu.cpt.gff3.fixsixpack" title="Properly formats naive ORF caller output for Apollo"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GFF3 Add Gene to CDS for Sixpack</button></a>
@@ -755,13 +824,14 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=tsebra" title="tanscript selector for BRAKER"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">TSEBRA</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=windowmasker_mkcounts" title="Construct WindowMasker unit counts table"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">WindowMasker mkcounts</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=windowmasker_ustat" title="Mask sequences using a WindowMasker unit counts table"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">WindowMasker ustat</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=orthofinder_onlygroups" title="finds orthogroups in a set of proteomes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">OrthoFinder</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=panaroo" title="A Bacterial Pangenome Analysis Pipeline"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Panaroo</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=tapscan_classify" title="Detect Transcription Associated Proteins (TAPs)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">TAPScan Classify</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=aegean_canongff3" title="pre-process GFF3 files, removing all features not directly related to protein-coding genes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">AEGeAn CanonGFF3</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=aegean_locuspocus" title="calculate locus coordinates for the given gene annotation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">AEGeAn LocusPocus</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=aegean_parseval" title="compare two sets of gene annotations for the same sequence."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">AEGeAn ParsEval</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=aegean_gaeval" title="compute coverage and integrity scores for gene models using transcript alignments."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">AEGeAn GAEVAL</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=edu.tamu.cpt.fasta.seq_trans" title="Translate fasta file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Fasta Translate</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=omark" title="proteome quality assessment"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">OMArk</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=krocus" title="Multi-locus sequence typing (MLST) from uncorrected long reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">krocus</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=mirmachine" title="A tool to detect miRNA homologs in genome sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MirMachine</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=prodigal" title="A tool for gene prediction in microbial genomes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Prodigal Gene Predictor</button></a>
@@ -782,106 +852,53 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=argnorm" title="a tool to normalize antibiotic resistance genes (ARGs) by mapping them to the antibiotic resistance ontology (ARO)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">argNorm</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=evidencemodeler" title="combines ab intio gene predictions, protein and transcript alignments into gene structures"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">EVidenceModeler</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=groot" title="align reads to references and weight variation graphs and generate report"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Groot</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=tetyper" title="Transposable Element Typer"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">TETyper</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ectyper" title="ectyper is a standalone serotyping module for Escherichia coli. It supports fasta and fastq file formats."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ectyper</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=staramr_search" title="Scans genome assemblies against the ResFinder, PlasmidFinder, and PointFinder databases searching for AMR genes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">staramr</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ppanggolin_all" title="generates a partitioned pangenome"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PPanGGOLiN all</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ppanggolin_msa" title="computes MSA of pangenome's gene families"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PPanGGOLiN MSA</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=hicexplorer_hicbuildmatrixmicroc" title="create a contact matrix"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hicBuildMatrixMicroC</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=deeparg_short_reads" title="pipeline to detect Antibiotic Resistance Genes (ARGs) from raw reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">DeepARG short reads</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=autobigs-cli" title="Automated MLST typing"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">autoBIGS.cli</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=mmseqs2_taxonomy_assignment" title="of sequences by comparing them to a reference database"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MMseqs2 Taxonomy Assignments</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=panaroo" title="A Bacterial Pangenome Analysis Pipeline"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Panaroo</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=icescreen" title="annotates ICEs and IMEs in Bacillota genomes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ICEscreen</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=gff_to_prot" title="to prot_table for TRANSIT"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert GFF3</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=tbl2gff3" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Table to GFF3</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=progressivemauve" title="constructs multiple genome alignments"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">progressiveMauve</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=xmfa2gff3" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert XMFA to gapped GFF3</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bp_genbank2gff3" title="converter"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Genbank to GFF3</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=exonerate" title="pairwise sequence comparison"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Exonerate</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=fastani" title="fast alignment-free computation of whole-genome Average Nucleotide Identity"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FastANI</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=fargene" title="Fragmented antibiotic resistance gene identifier"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">fargene</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=kobas_annotate" title="KEGG Orthology Based Annotation System"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">KOBAS Annotate</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=kobas_identify" title="KEGG Orthology Based Annotation System"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">KOBAS Identify</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=gprofiler_snpense" title="maps SNP rs-codes to gene names, chromosomal coordinates and variant effects"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">gProfiler SNPense</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=gprofiler_random" title="generates a gene list"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">gProfiler Random</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=gprofiler_gost" title="performs functional enrichment analysis of gene lists"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">gProfiler GOSt</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=gprofiler_orth" title="translates gene identifiers between organisms"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">gProfiler Orth</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=gprofiler_convert" title="converts between various types of namespaces"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">gProfiler Convert</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=abricate" title="Mass screening of contigs for antimicrobial and virulence genes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ABRicate</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=abricate_list" title="List all of abricate's available databases."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ABRicate List</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=blastxml_to_gapped_gff3" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BlastXML to gapped GFF3</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=Add_a_column1" title="an expression on every row"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Compute</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=socru" title="Calculate the order and orientation of complete bacterial genomes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">socru</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=snap_training" title="ab-initio gene predictor"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Train SNAP</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=maker_map_ids" title="on a Maker annotation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Map annotation ids</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=fgsea" title="- fast preranked gene set enrichment analysis"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">fgsea</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=goslimmer" title="converts a set of annotation from GO to a given GOSlim version"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GOSlimmer</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=goenrichment" title="performs GO enrichment analysis of a set of gene products"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GOEnrichment</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=jcvi_gff_stats" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Genome annotation statistics</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=picrust_metagenome_contributions" title="of OTUs to user-specified functions"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Metagenome Contributions</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=picrust_format_tree_and_trait_table" title="tree and trait tables"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Format</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=picrust_compare_biom" title="Compare the accuracy of biom files (expected and observed) either by observations (default) or by samples."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Compare BIOM tables</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=picrust_predict_metagenomes" title="based on the abundance of OTUs and a functional database"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Predict Metagenome</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=picrust_categorize" title="by collapsing hierarchical data to a specified functional level"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Categorize</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=trnascan" title="(tRNAscan)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">tRNA prediction</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=transtermhp" title="finds rho-independent transcription terminators in bacterial genomes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">TransTermHP</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=smf_utils_estimate-energy" title="Estimates whether a certain Segment(Loop) is present and for which delta-G this transistion takes place"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">estimate-energy</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=smf_utils_fix-fasta-headers" title="Replaces all spaces with underscores in the '>..'-sequence headers of a FASTA file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">fix-fasta-headers</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=smf_utils_filter-annotated-entries" title="Split entries into two files based on whether they overlap annotations in a bed file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">filter-annotated-entries</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=smf_utils_add-read-counts" title="Annotate sequences by adding the read counts from a bam file, within a region contained in the fasta header of the dbn file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">add-read-counts</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=smf_utils_find-boxes" title="Finds all occurances of two given boxes (sequence motifs) within a FASTA file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">find-boxes</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=smf_utils_filter-by-energy" title="Split entries over two files based on the estimated energy"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">filter-by-energy</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=smf_utils_extract-boxed-sequences" title="Extracts boxed sequences from bed_input_file which has to be created with 'find-box', part of this utility"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">extract-boxed-sequences</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=segmentation_fold" title="RNA-Folding including predefined segments including K-turns"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">segmentation-fold</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bg_sortmerna" title="of ribosomal RNAs in metatranscriptomic data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Filter with SortMeRNA</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=Probmetab" title="Wrapper function for ProbMetab R package."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ProbMetab Tool</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=lcmsmatching" title="Annotation of MS peaks using matching on a spectra database."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">LC/MS matching</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=Nucleosome" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Nucleosome Predictions</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=miranda" title="finds potential target sites for miRNAs in genomic sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">miRanda</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=dotknot" title="pseudoknot prediction in a given RNA sequence"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">DotKnot</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bg_find_subsequences" title="providing regions in BED format"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Nucleotide subsequence search</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=rbc_gotohscan" title="Find subsequences in db"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GotohScan</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=deeparg_predict" title="Antibiotic Resistance Genes (ARGs) from metagenomes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">DeepARG predict</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ncbi_egapx" title="annotates eukaryotic genomes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NCBI EGAPx</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ppanggolin_projection" title="annotates external genomes using an existing pangenome"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PPanGGOLiN projection</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ppanggolin_rarefaction" title="computes the rarefaction curve of the pangenome"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PPanGGOLiN rarefaction</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=tb_profiler_collate" title="Combines multiple TB-Profiler JSON reports into summary and variants reports"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">TB-Profiler Collate</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=panta" title="Efficient inference of large prokaryotic pangenomes with PanTA"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PanTA</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ncbi_fcs_adaptor" title="detects contamination from foreign organisms in genome sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NCBI FCS Adaptor</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=trnascan" title="using tRNAscan, EufindtRNA & tRNA covariance models"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">tRNA prediction</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=aragorn_trna" title="prediction (Aragorn)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">tRNA and tmRNA</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=psortb" title="Protein subcellular localization prediction for prokaryotes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PSORTb</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=fastoma" title="Infer orthology relationships"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FastOMA</button></a>
 <h3 id="multiplealignments">Multiple Alignments</h3>
-<a href="https://usegalaxy.eu/root?tool_id=rbc_mafft_add" title="Align a sequence,alignment or fragments to an existing alignment."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MAFFT add</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=rbc_mafft" title="Multiple alignment program for amino acid or nucleotide sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MAFFT</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=mummer_delta_filter" title="Filters alignment (delta) file from nucmer"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Delta-Filter</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=mummer_show_coords" title="Parse delta file and report coordinates and other information"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Show-Coords</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=clustalw" title="multiple sequence alignment program for DNA or proteins"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ClustalW</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=sina" title="reference based multiple sequence alignment"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SINA</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=gecko" title="Ungapped genome comparison"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Gecko</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=maf_stats1" title="Alignment coverage information"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MAF Coverage Stats</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=mummer_mummer" title="Align two or more sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Mummer</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=mummer_mummerplot" title="Generate 2-D dotplot of aligned sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Mummerplot</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=mummer_delta_filter" title="Filters alignment (delta) file from nucmer"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Delta-Filter</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=mummer_nucmer" title="Align two or more sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Nucmer</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=mummer_dnadiff" title="Evaluate similarities/differences between two sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">DNAdiff</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=mummer_show_coords" title="Parse delta file and report coordinates and other information"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Show-Coords</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=kc-align" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Kc-Align</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=chromeister" title="ultra-fast pairwise genome comparisons"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Chromeister</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=pipelign" title="alignment with pipelign"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Automated multiple sequence</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=mmseqs2_easy_linclust_clustering" title="of very large datasets"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MMseqs2 Sequence Clustering</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=selectsequencesfrommsa" title="Tool to select representative sequences from a multiple sequence alignment."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Select Sequences</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=msaboot" title="Output PHYLIP file with bootstrapped multiple sequence alignment data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MSABOOT</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=hammock_1.0" title="Clusters short peptide sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Hammock - cluster peptides</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=format_cd_hit_output" title="to rename representative sequences with cluster name and/or extract distribution inside clusters given a mapping file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Format cd-hit outputs</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=muscle" title="multiple aligner"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MUSCLE</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=compalignp" title="Fractional identities between alignments"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Compalignp</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=rbc_mafft" title="Multiple alignment program for amino acid or nucleotide sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MAFFT</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=rbc_mafft_add" title="Align a sequence,alignment or fragments to an existing alignment."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MAFFT add</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=cd_hit" title="Cluster or compare biological sequence datasets"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">cd-hit</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=mashmap" title="Fast local alignment boundaries"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">mashmap</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=trimal" title="for automated alignment trimming"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">trimAl</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=mmseqs2_easy_linclust_clustering" title="of very large datasets"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MMseqs2 Sequence Clustering</button></a>
 <h3 id="assembly">Assembly</h3>
-<a href="https://usegalaxy.eu/root?tool_id=minipolish" title="polishing miniasm assemblies"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">minipolish</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=spades_rnaviralspades" title="de novo assembler for transcriptomes, metatranscriptomes and metaviromes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">rnaviralSPAdes</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=spades_metaplasmidspades" title="extract and assembly plasmids from metagenomic data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">metaplasmidSPAdes</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=spades_biosyntheticspades" title="biosynthetic gene cluster assembly"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">biosyntheticSPAdes</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=flye" title="de novo assembler for single molecule sequencing reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Flye</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=rnaspades" title="de novo transcriptome assembler"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">rnaSPAdes</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=fastk_logex" title="Performs binary operations on the generated Ktab files from FASTK suite"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FastK Logex</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=mitohifi" title="Assemble mitogenomes from Pacbio HiFi reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MitoHiFi</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=hifiasm" title="haplotype-resolved de novo assembler for PacBio Hifi reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Hifiasm</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=spades_coronaspades" title="SARS-CoV-2 de novo genome assembler"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">coronaSPAdes</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=spades" title="genome assembler for genomes of regular and single-cell projects"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SPAdes</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=fastk_histex" title="Reads and displays a kmer histogram produced by FastK"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FastK Histex</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=meryl_arithmetic_kmers" title="apply arithmetic operations to k-mer counts"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Meryl</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=fastk_fastk" title="A k-mer counter for high-quality assembly datasets"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FastK</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=trycycler_cluster" title="cluster the contigs of your input assemblies into per-replicon groups"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Trycycler cluster</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=trycycler_consensus" title="generate a consensus contig sequence for each cluster"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Trycycler consensus</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=trycycler_partition" title="assign the reads to the clusters"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Trycycler partition</button></a>
@@ -904,17 +921,20 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=shovill" title="Faster SPAdes assembly of Illumina reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Shovill</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=racon" title="Consensus module for raw de novo DNA assembly of long uncorrected reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Racon</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=minia" title="Short-read assembler based on a de Bruijn graph"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Minia</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=flye" title="de novo assembler for single molecule sequencing reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Flye</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=quast" title="Genome assembly Quality"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Quast</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=miniasm" title="Ultrafast de novo assembly for long noisy reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">miniasm</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=abyss-pe" title="de novo sequence assembler"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ABySS</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=unicycler" title="pipeline for bacterial genomes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Create assemblies with Unicycler</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=idba_ud" title="Iterative de Bruijn Graph Assembler for data with highly uneven depth"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">IDBA-UD</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=idba_hybrid" title="Iterative de Bruijn Graph Assembler for hybrid sequencing data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">IDBA-HYBRID</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=spades" title="genome assembler for genomes of regular and single-cell projects"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SPAdes</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=velvetoptimiser" title="Automatically optimize Velvet assemblies"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VelvetOptimiser</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=pilon" title="An automated genome assembly improvement and variant detection tool"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">pilon</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=wtdbg" title="Fast de novo sequence assembler for long noisy reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">WTDBG2</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=metaspades" title="metagenome assembler"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">metaSPAdes</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=disco" title="to assemble metagenomics data using an overlap-layout-consensus (OLC) approach"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">DISCO</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=rnaspades" title="de novo transcriptome assembler"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">rnaSPAdes</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=meryl" title="a genomic k-mer counter and sequence utility"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Meryl</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=mira_assembler" title="Takes Sanger, Roche, Illumina, and Ion Torrent data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Assemble with MIRA v3.4</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=rna_quast" title="A quality assessment tool for De Novo transcriptome assemblies"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">rnaQUAST</button></a>
@@ -925,16 +945,22 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=ssake" title="short DNA sequences assembler"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SSAKE</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=crispr_recognition_tool" title="(CRT)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CRISPR Recognition Tool</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=minced" title="(minced)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">detect CRISPR sequences</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=velveth" title="Prepare a dataset for the Velvet velvetg Assembler"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">velveth</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=genomescope" title="reference-free genome profiling"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GenomeScope</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=pretext_map" title="converts SAM or BAM files into genome contact maps"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PretextMap</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=bionano_scaffold" title="automates the scaffolding process"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Bionano Hybrid Scaffold</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=bellerophon" title="chimeric reads from Arima Genomics"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Filter and merge</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=mitohifi" title="Assemble mitogenomes from Pacbio HiFi reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MitoHiFi</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=raven" title="De novo assembly of Oxford Nanopore Technologies data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Raven</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ragtag" title="reference-guided scaffolding of draft genomes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RagTag</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=tgsgapcloser" title="fills the N-gap of error-prone long reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">TGS-GapCloser</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=hypo" title="super fast and accurate polisher for long read genome assemblies"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">HyPo</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=spades_rnaviralspades" title="de novo assembler for transcriptomes, metatranscriptomes and metaviromes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">rnaviralSPAdes</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=spades_plasmidspades" title="extract and assembly plasmids from WGS data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">plasmidSPAdes</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=spades_metaviralspades" title="extract and assembly viral genomes from metagenomic data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">metaviralSPAdes</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=spades_metaplasmidspades" title="extract and assembly plasmids from metagenomic data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">metaplasmidSPAdes</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=spades_coronaspades" title="SARS-CoV-2 de novo genome assembler"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">coronaSPAdes</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=spades_biosyntheticspades" title="biosynthetic gene cluster assembly"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">biosyntheticSPAdes</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=links" title="- scaffold genome assemblies with long reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">LINKS</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=gfastats" title="the swiss army knife for genome assembly"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">gfastats</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=merqury" title="evaluate the assembly quality"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Merqury</button></a>
@@ -945,6 +971,7 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=smudgeplot" title="inference of ploidy and heterozygosity structure using whole genome sequencing"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Smudgeplot</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=hapog" title="genome polishing"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Hapo-G</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=get_organelle_from_reads" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Get organelle from reads</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=minipolish" title="polishing miniasm assemblies"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">minipolish</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=cactus_cactus" title="whole-genome multiple sequence alignment"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Cactus</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=cactus_export" title="whole-genome multiple sequence alignment to other formats"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Cactus: export</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=instagraal" title="Large genome reassembly based on Hi-C data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">instaGRAAL</button></a>
@@ -956,145 +983,110 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=get_annotated_regions_from_gb" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Get annotated regions from genbank files (getorganelle)</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=aligned_to_consensus" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Consensus sequence from aligned FASTA</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=verkko" title="hybrid genome assembly pipeline"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">verkko</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=velveth" title="Prepare a dataset for the Velvet velvetg Assembler"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">velveth</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=merquryplot" title="evaluate the assembly quality"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Merqury histogram plot</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=pretext_graph" title="Embed bedgraph formatted data inside a Pretext contact map."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Pretextgraph</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=pairtools_dedup" title="Find and remove PCR/optical duplicates"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Pairtools dedup</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=pairtools_parse" title="Find ligation pairs in alignments and create pairs."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Pairtools parse</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=pairtools_split" title="Split a pairsam file into pairs and SAM/BAM"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Pairtools split</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=pairtools_sort" title="Sort a 4dn pairs/pairsam file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Pairtools sort</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=pairtools_stats" title="Calculates pairs statistics for input pairs and pairsam files."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Pairtools Stats</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=reago" title="to assemble rRNA"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Reago</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=fastk_fastk" title="A k-mer counter for high-quality assembly datasets"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FastK</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=refseq_masher_contains" title="Find NCBI RefSeq Genomes contained in your sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RefSeq Masher Contains</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=refseq_masher_matches" title="Find closest matching NCBI RefSeq Genomes to your sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RefSeq Masher Matches</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=make_ear" title="A tool to compile assembly reports and statistics from assembly pipeline"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ERGA Assembly Reporting Tool (EAR)</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=fastk_logex" title="Performs binary operations on the generated Ktab files from FASTK suite"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FastK Logex</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=fastk_histex" title="Reads and displays a kmer histogram produced by FastK"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FastK Histex</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=meryl_count_kmers" title="count k-mers"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Meryl</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=meryl_filter_kmers" title="filter k-mers"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Meryl</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=meryl_histogram_kmers" title="get k-mer frequency histogram"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Meryl</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=meryl_groups_kmers" title="apply operations on k-mer databases"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Meryl</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=meryl_trio_mode" title="build hap-mers databases for trios"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Meryl</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=meryl_print" title="get k-mer counts"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Meryl</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=meryl_arithmetic_kmers" title="apply arithmetic operations to k-mer counts"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Meryl</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=syri" title="Synteny and Rearrangement Identifier"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SyRI</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=fbqs_integrator" title="Merge quality-checked outputs from Fastp, Bracken and QUAST into consolidated STARAMR Excel report"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FBQS Integrator</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=merquryplot" title="evaluate the assembly quality"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Merqury histogram plot</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=pretext_graph" title="Embed bedgraph formatted data inside a Pretext contact map."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Pretextgraph</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=reago" title="to assemble rRNA"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Reago</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=refseq_masher_contains" title="Find NCBI RefSeq Genomes contained in your sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RefSeq Masher Contains</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=refseq_masher_matches" title="Find closest matching NCBI RefSeq Genomes to your sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RefSeq Masher Matches</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=make_ear" title="A tool to compile assembly reports and statistics from assembly pipeline"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ERGA Assembly Reporting Tool (EAR)</button></a>
 <h3 id="mapping">Mapping</h3>
+<a href="https://usegalaxy.eu/root?tool_id=parabricks_fq2bam" title="Run GPU-bwa mem mapper"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Parabricks fq2bam</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=megablast_xml_parser" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Parse blast XML output</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=rna_star" title="Gapped-read mapper for RNA-seq data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RNA STAR</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=rna_starsolo" title="mapping, demultiplexing and gene quantification for single cell RNA-seq"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RNA STARSolo</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=minimap2" title="A fast pairwise aligner for genomic and spliced nucleotide sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Map with minimap2</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=lastz_wrapper_2" title=": align long sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">LASTZ</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=megablast_wrapper" title="compare short reads against htgs, nt, and wgs databases"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Megablast</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=winnowmap" title="a mapping tool optimized for repetitive sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Winnowmap</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=lastz_paired_reads_wrapper" title="map short paired reads against reference sequence"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Lastz paired reads</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bioext_bealign" title="to a reference using a codon alignment algorithm"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Align sequences</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=hisat2" title="A fast and sensitive alignment program"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">HISAT2</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=lastz_wrapper_2" title=": align long sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">LASTZ</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=bowtie_wrapper" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Map with Bowtie for Illumina</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=lastz_d_wrapper" title=": estimate substitution scores matrix"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">LASTZ_D</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bbtools_bbmap" title="short-read aligner"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BBTools: BBMap</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bowtie2" title="- map reads against reference genome"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Bowtie2</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bwa_mem2" title="- map medium and long reads (> 100 bp) against reference genome"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BWA-MEM2</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=pbmm2" title="map PacBio reads to a reference genome."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">pbmm2</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bwameth" title="Fast and accurate aligner of BS-Seq reads."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bwameth</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bwa_mem" title="- map medium and long reads (> 100 bp) against reference genome"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Map with BWA-MEM</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bwa" title="- map short reads (< 100 bp) against reference genome"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Map with BWA</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=kma_map" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Map with KMA</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bwa_mem2_idx" title="Build BWA-MEM2 reference index"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BWA-MEM2 indexer</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=minimap2" title="A fast pairwise aligner for genomic and spliced nucleotide sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Map with minimap2</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=hisat2" title="A fast and sensitive alignment program"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">HISAT2</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=rna_starsolo" title="mapping, demultiplexing and gene quantification for single cell RNA-seq"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RNA STARSolo</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=rna_star" title="Gapped-read mapper for RNA-seq data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RNA STAR</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=bismark_bowtie2" title="Bisulfite reads mapper"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Bismark Mapper</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=kma_map" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Map with KMA</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=star_fusion" title="detect fusion genes in RNA-Seq data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">STAR-Fusion</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=bismark_deduplicate" title="Deduplicates reads mapped by Bismark"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Bismark Deduplicate</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=bismark_pretty_report" title="Generates a graphical HTML report page from report outputs of Bismark"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Bismark Pretty Report</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=bismark_methylation_extractor" title="Reports on methylation status of reads mapped by Bismark"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Bismark Meth. Extractor</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bowtie2" title="- map reads against reference genome"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Bowtie2</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=segemehl" title="short read mapping with gaps"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">segemehl</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=graphmap_overlap" title="fast, trimmed overlap pipeline without aligning"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Owler</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=graphmap_align" title="for long, error-prone reads, like Nanopore ONT and PacBio"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Mapper</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bwa" title="- map short reads (< 100 bp) against reference genome"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Map with BWA</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bwa_mem" title="- map medium and long reads (> 100 bp) against reference genome"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Map with BWA-MEM</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=lastz_d_wrapper" title=": estimate substitution scores matrix"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">LASTZ_D</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bwameth" title="Fast and accurate aligner of BS-Seq reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bwameth</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=tophat2" title="Gapped-read mapper for RNA-seq data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">TopHat</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=bowtie_color_wrapper" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Map with Bowtie for SOLiD</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=winnowmap" title="a mapping tool optimized for repetitive sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Winnowmap</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bioext_bealign" title="to a reference using a codon alignment algorithm"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Align sequences</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bwa_mem2" title="- map medium and long reads (> 100 bp) against reference genome"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BWA-MEM2</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=bfast_wrapper" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Map with BFAST</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bbtools_bbmap" title="short-read aligner"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BBTools: BBMap</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=pbmm2" title="map PacBio reads to a reference genome."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">pbmm2</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bwa_mem2_idx" title="Build BWA-MEM2 reference index"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BWA-MEM2 indexer</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=PerM" title="for SOLiD and Illumina"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Map with PerM</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=srma_wrapper" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Re-align with SRMA</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=mosaik_wrapper" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Map with Mosaik</button></a>
 <h3 id="variantcalling">Variant Calling</h3>
-<a href="https://usegalaxy.eu/root?tool_id=ensembl_vep" title="with VEP"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Predict variant effects</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=freebayes" title="bayesian genetic variant detector"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FreeBayes</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bamleftalign" title="indels in BAM datasets"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BamLeftAlign</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=smgu_frameshift_deletions_checks" title="reports on frameshifting indels in consensus sequence"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Frameshift Deletions Checks</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=cnvkit_target" title="Prepare a BED file of baited regions for use with CNVkit"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CNVkit Target</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=cnvkit_genemetrics" title="Identify targeted genes with copy number gain or loss"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CNVkit Genemetrics</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=cnvkit_theta" title="Convert segments to THetA2 input file format"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CNVkit Theta</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=cnvkit_call" title="Call copy number variants from segmented log2 ratios"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CNVkit Call</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bbtools_callvariants" title="in aligned Bam files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BBTools: call variants</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=naive_variant_caller" title="- tabulate variable sites from BAM datasets"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Naive Variant Caller (NVC)</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bcftools_plugin_split_vep" title="plugin Extracts fields from structured annotations such as INFO/CSQ"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bcftools split-vep</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=allele_counts_1" title="process variant counts"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Variant Annotator</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=snpSift_int" title="Filter variants using intervals"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SnpSift Intervals</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=snpEff" title="annotate variants"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SnpEff eff:</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=snpSift_annotate" title="SNPs from dbSnp"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SnpSift Annotate</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=snpSift_filter" title="Filter variants using arbitrary expressions"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SnpSift Filter</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=snpSift_caseControl" title="Count samples are in 'case' and 'control' groups."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SnpSift CaseControl</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=get_hrun" title="Annotate indel variants with homopolymer context"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Get homopolymer run length</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=snippy_core" title="Combine multiple Snippy outputs into a core SNP alignment"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">snippy-core</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=snippy" title="Snippy finds SNPs between a haploid reference genome and your NGS sequence reads."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">snippy</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=snippy_clean_full_aln" title="Replace any non-standard sequence characters in snippy 'core.full.aln' file."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">snippy-clean_full_aln</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=sansa_annotate" title="structural variants"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">sansa annotate</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=jasminesv" title="Merge structural variants across samples"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">JasmineSV</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=irissv" title="Refine insertion sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Iris</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bcftools_mpileup" title="Generate VCF or BCF containing genotype likelihoods for one or multiple alignment (BAM or CRAM) files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bcftools mpileup</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bcftools_view" title="VCF/BCF conversion, view, subset and filter VCF/BCF files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bcftools view</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bcftools_stats" title="Parses VCF or BCF and produces stats which can be plotted using plot-vcfstats"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bcftools stats</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bcftools_roh" title="HMM model for detecting runs of homo/autozygosity"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bcftools roh</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bcftools_reheader" title="Modify header of VCF/BCF files, change sample names"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bcftools reheader</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bcftools_query" title="Extracts fields from VCF/BCF file and prints them in user-defined format"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bcftools query</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bcftools_isec" title="Create intersections, unions and complements of VCF files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bcftools isec</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bcftools_gtcheck" title="Check sample identity"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bcftools gtcheck</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bcftools_filter" title="Apply fixed-threshold filters"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bcftools filter</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bcftools_convert_to_vcf" title="Converts other formats to VCF/BCFk"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bcftools convert to vcf</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bcftools_convert_from_vcf" title="Converts VCF/BCF to IMPUTE2/SHAPEIT formats"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bcftools convert from vcf</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bcftools_annotate" title="Annotate and edit VCF/BCF files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bcftools annotate</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=beagle" title="phasing genotypes and imputing ungenotyped markers"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Beagle</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=lumpy_prep" title="extracts discordant read pairs and split-read alignments from a BAM dataset"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">LUMPY preprocessing</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=lumpy_sv" title="is a probabilistic framework for structural variant discovery"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">LUMPY</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=seqwish" title="Alignment to variation graph inducer"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">seqwish</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=deepvariant" title="deep learning-based variant caller"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">DeepVariant</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=gatk4_mutect2" title="- Call somatic SNVs and indels via local assembly of haplotypes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GATK4 Mutect2</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bcftools_cnv" title="Call copy number variation from VCF B-allele frequency (BAF) and Log R Ratio intensity (LRR) values"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bcftools cnv</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=control_freec" title="detects copy-number changes and allelic imbalances"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Control-FREEC</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=king" title="Kinship-based INference for GWAS"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">KING</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=vardict_java" title="calls SNVs and indels for tumor-normal pairs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VarDict</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=delly_cnv" title="discover and genotype copy-number variants"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Delly cnv</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=delly_classify" title="somatic or germline copy-number variants"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Delly classify</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=delly_lr" title="optimized calling and genotyping of structural variants"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Delly long-read (lr)</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=delly_call" title="and genotype structural variants"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Delly call</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=delly_merge" title="structural variants across/within BCF/VCF file(s)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Delly merge</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=delly_filter" title="somatic or germline structural variants"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Delly filter</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=artic_guppyplex" title="Filter Nanopore reads by read length and (optionally) quality"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ARTIC guppyplex</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=artic_minion" title="Build consensus sequence and call variants from amplicon-based nanopore sequence data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ARTIC minion</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=plink" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">plink</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bcftools_concat" title="Concatenate or combine VCF/BCF files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bcftools concat</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=varscan_mpileup" title="for variant detection"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VarScan mpileup</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bcftools_merge" title="Merge multiple VCF/BCF files from non-overlapping sample sets to create one multi-sample file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bcftools merge</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=pharmcat" title="Pharmacogenomics Clinical Annotation Tool"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">pharmCAT</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=cnvkit_heatmap" title="Plot copy number for multiple samples as a heatmap"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CNVkit Heatmap</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=cnvkit_batch" title="Run the CNVkit pipeline on one or more BAM files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CNVkit Batch</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=fatovcf" title="Convert a FASTA alignment file to Variant Call Format (VCF) single-nucleotide diffs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">faToVcf</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=manta" title="Manta calls structural variants (SVs) and indels from mapped paired-end sequencing reads."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Manta</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=strelka_germline" title="small variant caller for germline variation in small cohorts"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Strelka Germline</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=sansa_annotate" title="structural variants"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">sansa annotate</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=strelka_somatic" title="small variant caller for somatic variation in tumor/normal sample pairs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Strelka Somatic</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=delly_filter" title="somatic or germline structural variants"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Delly filter</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=delly_merge" title="structural variants across/within BCF/VCF file(s)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Delly merge</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=delly_call" title="and genotype structural variants"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Delly call</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=delly_lr" title="optimized calling and genotyping of structural variants"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Delly long-read (lr)</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=bcftools_consensus" title="Create consensus sequence by applying VCF variants to a reference fasta file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bcftools consensus</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=delly_classify" title="somatic or germline copy-number variants"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Delly classify</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=delly_cnv" title="discover and genotype copy-number variants"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Delly cnv</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=vcfanno" title="VCF annotation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">vcfanno</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=jasminesv" title="Merge structural variants across samples"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">JasmineSV</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=irissv" title="Refine insertion sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Iris</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=mut2read" title="Extracts all tags that carry a mutation in the duplex consensus sequence (DCS)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">DCS mutations to tags/reads:</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=mut2sscs" title="Extracts all tags from the single stranded consensus sequence (SSCS) bam file that carry a mutation at the same position a mutation is called in the duplex consensus sequence (DCS) and calculates their frequencies"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">DCS mutations to SSCS stats:</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=read2mut" title="Looks for reads with mutation at known positions and calculates frequencies and stats."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Call specific mutations in reads:</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=snpSift_filter" title="Filter variants using arbitrary expressions"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SnpSift Filter</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=lumpy_sv" title="is a probabilistic framework for structural variant discovery"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">LUMPY</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=lumpy_prep" title="extracts discordant read pairs and split-read alignments from a BAM dataset"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">LUMPY preprocessing</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=lofreq_filter" title="called variants posteriorly"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Lofreq filter</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=lofreq_call" title="with LoFreq"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Call variants</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=plink" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">plink</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=artic_minion" title="Build consensus sequence and call variants from amplicon-based nanopore sequence data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ARTIC minion</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=cutesv" title="detects long-read-based SVs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">cuteSV</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=vardict_java" title="calls SNVs and indels for tumor-normal pairs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VarDict</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=control_freec" title="detects copy-number changes and allelic imbalances"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Control-FREEC</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=gatk4_mutect2" title="- Call somatic SNVs and indels via local assembly of haplotypes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GATK4 Mutect2</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bcftools_concat" title="Concatenate or combine VCF/BCF files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bcftools concat</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=snpeff_sars_cov_2" title="annotate variants for SARS-CoV-2"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SnpEff eff:</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=lofreq_viterbi" title="with LoFreq viterbi"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Realign reads</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=lofreq_alnqual" title="to aligned read SAM/BAM records"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Add LoFreq alignment quality scores</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=lofreq_indelqual" title="into a BAM file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Insert indel qualities</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=seqwish" title="Alignment to variation graph inducer"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">seqwish</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=odgi_viz" title="variation graph visualizations"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">odgi viz</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=odgi_build" title="construct a dynamic succinct variation graph"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">odgi build</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=vg_view" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">vg view</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=vg_deconstruct" title="construct a dynamic succinct variation graph"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">vg deconstruct</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=vg_convert" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">vg convert</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=snippy_core" title="Combine multiple Snippy outputs into a core SNP alignment"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">snippy-core</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=snippy_clean_full_aln" title="Replace any non-standard sequence characters in snippy 'core.full.aln' file."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">snippy-clean_full_aln</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=snippy" title="Snippy finds SNPs between a haploid reference genome and your NGS sequence reads."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">snippy</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bcftools_merge" title="Merge multiple VCF/BCF files from non-overlapping sample sets to create one multi-sample file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bcftools merge</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=vcfselectsamples" title="Select samples from a VCF dataset"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VCFselectsamples:</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=vcfannotategenotypes" title="Annotate genotypes in a VCF dataset using genotypes from another VCF dataset"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VCFannotateGenotypes:</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=vcfdistance" title="Calculate distance to the nearest variant"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VCFdistance:</button></a>
@@ -1123,10 +1115,12 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=bcftools_csq" title="Haplotype aware consequence predictor"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bcftools csq</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=bcftools_plugin_frameshifts" title="plugin Annotate frameshift indels"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bcftools frameshifts</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=bcftools_plugin_color_chrs" title="plugin Color shared chromosomal segments, requires phased GTs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bcftools color-chrs</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bcftools_cnv" title="Call copy number variation from VCF B-allele frequency (BAF) and Log R Ratio intensity (LRR) values"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bcftools cnv</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=snp_dists" title="Compute distance in SNPs between all sequences in a FASTA file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SNP distance matrix</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=tag_pileup_frequency" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Tag pileup frequency</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=snp_sites" title="from a multi-FASTA alignment file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Finds SNP sites</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=exomedepth" title="Calls copy number variants (CNVs) from targeted sequence data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ExomeDepth</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=freebayes" title="bayesian genetic variant detector"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FreeBayes</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=snpEff_build_gb" title="database from Genbank or GFF record"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SnpEff build:</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=varscan_somatic" title="Call germline/somatic and LOH variants from tumor-normal sample pairs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VarScan somatic</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=basil" title="Breakpoint detection, including large insertions"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">basil</button></a>
@@ -1139,45 +1133,74 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=snpSift_extractFields" title="from a VCF file into a tabular file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SnpSift Extract Fields</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=snpSift_vcfCheck" title="basic checks for VCF specification compliance"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SnpSift vcfCheck</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=bcfview" title="Convert, filter, subset VCF/BCF files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bcftoolsView</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bamleftalign" title="indels in BAM datasets"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BamLeftAlign</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=vt_normalize" title="normalizes variants in a VCF file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VT normalize</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=naive_variant_caller" title="- tabulate variable sites from BAM datasets"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Naive Variant Caller (NVC)</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=snpEff_databases" title="list available databases"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SnpEff databases:</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=snpSift_geneSets" title="Annotating GeneSets, such as Gene Ontology, KEGG, Reactome"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SnpSift GeneSets</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=snpSift_dbnsfp" title="Add annotations from dbNSFP or similar annotation DBs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SnpSift dbNSFP</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=snpSift_dbnsfp_generic" title="Add Annotations from dbNSFP and similar annotation DBs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SnpSift dbNSFP</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=snpEff_download" title="download a pre-built database"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SnpEff download:</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=snpEff" title="annotate variants"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SnpEff eff:</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=varscan_copynumber" title="Determine relative tumor copy number from tumor-normal pileups"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VarScan copynumber</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=varscan" title="for variant detection"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VarScan</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=varscan_mpileup" title="for variant detection"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VarScan mpileup</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=SnpEff-cds-report" title="Report Variant coding sequence changes for SnpEffects"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SnpEff Ensembl CDS</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=snpeff_to_peptides" title="to create a Search DB fasta for variant SAP peptides"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SnpEff to Peptide fasta</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bcftools_plugin_split_vep" title="plugin Extracts fields from structured annotations such as INFO/CSQ"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bcftools split-vep</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=allele_counts_1" title="process variant counts"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Variant Annotator</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=snpSift_int" title="Filter variants using intervals"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SnpSift Intervals</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=snpSift_annotate" title="SNPs from dbSnp"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SnpSift Annotate</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=snpSift_filter" title="Filter variants using arbitrary expressions"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SnpSift Filter</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=snpSift_caseControl" title="Count samples are in 'case' and 'control' groups."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SnpSift CaseControl</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=get_hrun" title="Annotate indel variants with homopolymer context"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Get homopolymer run length</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bcftools_mpileup" title="Generate VCF or BCF containing genotype likelihoods for one or multiple alignment (BAM or CRAM) files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bcftools mpileup</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bcftools_view" title="VCF/BCF conversion, view, subset and filter VCF/BCF files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bcftools view</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bcftools_stats" title="Parses VCF or BCF and produces stats which can be plotted using plot-vcfstats"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bcftools stats</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bcftools_roh" title="HMM model for detecting runs of homo/autozygosity"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bcftools roh</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bcftools_reheader" title="Modify header of VCF/BCF files, change sample names"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bcftools reheader</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bcftools_query" title="Extracts fields from VCF/BCF file and prints them in user-defined format"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bcftools query</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bcftools_isec" title="Create intersections, unions and complements of VCF files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bcftools isec</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bcftools_gtcheck" title="Check sample identity"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bcftools gtcheck</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bcftools_filter" title="Apply fixed-threshold filters"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bcftools filter</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bcftools_convert_to_vcf" title="Converts other formats to VCF/BCFk"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bcftools convert to vcf</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bcftools_convert_from_vcf" title="Converts VCF/BCF to IMPUTE2/SHAPEIT formats"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bcftools convert from vcf</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bcftools_annotate" title="Annotate and edit VCF/BCF files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bcftools annotate</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=beagle" title="phasing genotypes and imputing ungenotyped markers"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Beagle</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=deepvariant" title="deep learning-based variant caller"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">DeepVariant</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=king" title="Kinship-based INference for GWAS"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">KING</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=artic_guppyplex" title="Filter Nanopore reads by read length and (optionally) quality"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ARTIC guppyplex</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=pharmcat" title="Pharmacogenomics Clinical Annotation Tool"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">pharmCAT</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bbtools_callvariants" title="in aligned Bam files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BBTools: call variants</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ensembl_vep" title="with VEP"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Predict variant effects</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=breseq" title="find mutations in haploid microbial genomes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">breseq</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=vcf2maf" title="with vcf2maf"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert VCF to MAF</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bcftools_plugin_setgt" title="plugin Sets genotypes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bcftools setGT</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bcftools_plugin_setgt" title="plugin Sets genotypes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bcftools setGT</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=fatovcf" title="Convert a FASTA alignment file to Variant Call Format (VCF) single-nucleotide diffs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">faToVcf</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=cnvkit_access" title="Calculate the sequence-accessible coordinates in chromosomes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CNVkit Access</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=cnvkit_antitarget" title="Lists the chromosomal coordinates for targeted resequencing"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CNVkit Antitarget</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=cnvkit_autobin" title="Estimates read counts or depths in a BAM file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CNVkit Autobin</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cnvkit_batch" title="Run the CNVkit pipeline on one or more BAM files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CNVkit Batch</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cnvkit_call" title="Call copy number variants from segmented log2 ratios"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CNVkit Call</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=cnvkit_coverage" title="Calculate coverage in the given regions from BAM read depths"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CNVkit Coverage</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=cnvkit_diagram" title="Draw copy number on chromosomes as a diagram"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CNVkit Diagram</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=cnvkit_fix" title="Adjust raw coverage data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CNVkit Fix</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=cnvkit_breaks" title="List the targeted genes with segmentaion breakpoint"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CNVkit Breaks</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cnvkit_heatmap" title="Plot copy number for multiple samples as a heatmap"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CNVkit Heatmap</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=cnvkit_reference" title="Compile a copy-number reference from the given files or directory containing normal samples"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CNVkit Reference</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=cnvkit_scatter" title="Plot bin-level log2 coverages and segmentation calls together"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CNVkit Scatter</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=cnvkit_segment" title="Infer copy number segments from the given coverage table"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CNVkit Segment</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=cnvkit_segmetrics" title="calculate summary statistics"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CNVkit Segmetrics</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=cnvkit_sex" title="Guess samples’ chromosomal sex from the relative coverage of chromosomes X and Y"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CNVkit Sex</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=cnvkit_export_bed" title="Converts the Segmented copy ratio data file (*.cns) file into BED file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CNVkit Export BED</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=cnvkit_export_cdt" title="Convert log2 ratios to Clustered Data Table (CDT)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CNVkit Export CDT</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=cnvkit_export_jtv" title="Convert log2 ratios to Java TreeView's native format"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CNVkit Export JTV</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=cnvkit_export_nexus_basic" title="Convert bin-level log2 ratios to Nexus Copy Number 'basic' format"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CNVkit Export Nexus Basics</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=cnvkit_export_nexus_ogt" title="Convert log2 ratios and b-allele freqs to Nexus 'Custom-OGT' format"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CNVkit Export Nexus OGT</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=cnvkit_export_seg" title="Convert segments to Segment (SEG) format"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CNVkit Export SEG</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=cnvkit_export_vcf" title="Converts the Segmented copy ratio data file (*.cns) file into VCF file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CNVkit Export VCF</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=cnv_vcf2json" title="Converts the CNVkit structural variants VCF file to JSON"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CNV VCF2JSON</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bcftools_plugin_setgt" title="plugin Sets genotypes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bcftools setGT</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bcftools_plugin_setgt" title="plugin Sets genotypes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bcftools setGT</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cnvkit_target" title="Prepare a BED file of baited regions for use with CNVkit"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CNVkit Target</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=smgu_frameshift_deletions_checks" title="reports on frameshifting indels in consensus sequence"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Frameshift Deletions Checks</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=beacon2_csv2xlsx" title="v2 CSV Models to XLSX"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Beacon2 CSV2XLSX</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=beacon2_pxf2bff" title="converts Phenopacket PXF (JSON) to BFF (JSON)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Beacon2 PXF2BFF</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=beacon2_vcf2bff" title="converting annotated VCF files to Beacon v2 format"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Beacon2 VCF2BFF</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=manta" title="Manta calls structural variants (SVs) and indels from mapped paired-end sequencing reads."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Manta</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cnvkit_breaks" title="List the targeted genes with segmentaion breakpoint"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CNVkit Breaks</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cnvkit_genemetrics" title="Identify targeted genes with copy number gain or loss"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CNVkit Genemetrics</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cnvkit_segmetrics" title="calculate summary statistics"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CNVkit Segmetrics</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cnvkit_sex" title="Guess samples’ chromosomal sex from the relative coverage of chromosomes X and Y"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CNVkit Sex</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=cnv_phenopacket" title="Builds Phenopacket schema for the structural variants metadata from the 1000hg project"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CNV Phenopacket</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cnv_vcf2json" title="Converts the CNVkit structural variants VCF file to JSON"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CNV VCF2JSON</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=hgvsparser" title="parsing and building variant descriptor strings compliant with the HGVS standard"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hgvsParseR</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=beacon2_analyses" title="َQuery the analyses collection in the beacon database for bioinformatic procedures to identify variants"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Beacon2 Analyses</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=beacon2_biosamples" title="Query the biosamples collection in the beacon database for samples taken from individuals"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Beacon2 Biosamples</button></a>
@@ -1192,6 +1215,14 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=beacon2_runs" title="Query the runs collection in the beacon database"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Beacon2 Runs</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=beacon2_sequence" title="َQuery for the existence of a specified sequence at a given genomic position"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Beacon2 Sequence</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=sniffles" title="Structural variation caller using third generation sequencing"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">sniffles</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cnvkit_export_bed" title="Converts the Segmented copy ratio data file (*.cns) file into BED file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CNVkit Export BED</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cnvkit_export_cdt" title="Convert log2 ratios to Clustered Data Table (CDT)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CNVkit Export CDT</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cnvkit_export_jtv" title="Convert log2 ratios to Java TreeView's native format"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CNVkit Export JTV</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cnvkit_export_nexus_basic" title="Convert bin-level log2 ratios to Nexus Copy Number 'basic' format"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CNVkit Export Nexus Basics</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cnvkit_export_nexus_ogt" title="Convert log2 ratios and b-allele freqs to Nexus 'Custom-OGT' format"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CNVkit Export Nexus OGT</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cnvkit_export_seg" title="Convert segments to Segment (SEG) format"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CNVkit Export SEG</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cnvkit_theta" title="Convert segments to THetA2 input file format"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CNVkit Theta</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cnvkit_export_vcf" title="Converts the Segmented copy ratio data file (*.cns) file into VCF file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CNVkit Export VCF</button></a>
 <h3 id="genomeediting">Genome editing</h3>
 <a href="https://usegalaxy.eu/root?tool_id=crispr_studio" title="facilitate and accelerate CRISPR array visualization from a GFF3 file generated with CRISPRDetect"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CRISPR Studio</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=mageck_test" title="- given a table of read counts, perform the sgRNA and gene ranking"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MAGeCKs test</button></a>
@@ -1204,8 +1235,8 @@ layout: default
 <h3 id="rna-seq">RNA-Seq</h3>
 <a href="https://usegalaxy.eu/root?tool_id=blockbuster" title="detects blocks of overlapping reads using a gaussian-distribution approach"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">blockbuster</button></a>
 <h3 id="rnaanalysis">RNA Analysis</h3>
-<a href="https://usegalaxy.eu/root?tool_id=arriba_draw_fusions" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Arriba Draw Fusions</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=cemitool" title="gene co-expression network analyses"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CEMiTool</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=isoformswitchanalyzer" title="statistical identification of isoform switching"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">IsoformSwitchAnalyzeR</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=deseq2" title="Determines differentially expressed features from count tables"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">DESeq2</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=filter_combined_via_tracking" title="using tracking file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Filter Combined Transcripts</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=express" title="Quantify the abundances of a set of target sequences from sampled subsequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">eXpress</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=cuffmerge" title="merge together several Cufflinks assemblies"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Cuffmerge</button></a>
@@ -1231,7 +1262,6 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=cummeRbund" title="visualize Cuffdiff output"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">cummeRbund</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=htseq_count" title="- Count aligned reads in a BAM file that overlap features in a GFF file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">htseq-count</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=salmon" title="Perform dual-phase, reads or mapping-based estimation of transcript abundance from RNA-seq reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Salmon quant</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=deseq2" title="Determines differentially expressed features from count tables"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">DESeq2</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=stringtie" title="transcript assembly and quantification"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">StringTie</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=stringtie_merge" title="transcripts"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">StringTie merge</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=trinity_align_and_estimate_abundance" title="on a de novo assembly of RNA-Seq data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Align reads and estimate abundance</button></a>
@@ -1315,10 +1345,6 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=rseqc_inner_distance" title="calculate the inner distance (or insert size) between two paired RNA reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Inner Distance</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=rnaz" title="predicting structurally conserved and thermodynamically stable RNA secondary structures"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RNAz</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=RNAshapes" title="RNA Secondary structure prediction"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RNAshapes</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=arriba" title="detect gene fusions from STAR aligned RNA-Seq data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Arriba</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=infer_rnaformer" title="Predict the secondary structure of an RNA with RNAformer"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RNAformer</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=arriba_get_filters" title="to history"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Arriba Get Filters</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=sleuth" title="Differential expression analysis"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Sleuth</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=viennarna_rnafold" title="Calculate minimum free energy secondary structures and partition function of RNAs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RNAfold</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=idr" title="compare ranked list of identifications"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">IDR</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=viennarna_rnacofold" title="Calculate secondary structures of two RNAs with dimerization"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RNAcofold</button></a>
@@ -1383,15 +1409,20 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=rsem_prepare_reference" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RSEM prepare reference</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=rsem_calculate_expression" title="RNA-Seq by Expectation-Maximization"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RSEM calculate expression</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=extract_transcript_to_gene_map_from_trinity" title="extract transcript to gene map from trinity"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RSEM trinity fasta to gene map</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=infer_rnaformer" title="Predict the secondary structure of an RNA with RNAformer"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RNAformer</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=genomic_super_signature" title="interpretation of RNAseq experiments"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GenomicSuperSignature</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=barrnap" title="Locate ribosomal RNA's in a fasta file. (GFF output)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">barrnap</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=arriba_draw_fusions" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Arriba Draw Fusions</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=arriba_get_filters" title="to history"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Arriba Get Filters</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=arriba" title="detect gene fusions from STAR aligned RNA-Seq data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Arriba</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=circexplorer2" title="circular RNA analysis"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CIRCexplorer2</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ribowaltz_process" title="calculation of optimal P-site offsets and diagnostic analysis"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">riboWaltz</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ribowaltz_plot" title="visual inspection of ribosome profiling data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">riboWaltz-plot</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cemitool" title="gene co-expression network analyses"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CEMiTool</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=cherri_train" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Train a CheRRI model using RRIs</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=mirnature" title="Computational detection of canonical microRNAs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">miRNAture</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=cherri_eval" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Evaluation of RRIs using CheRRI</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=isoformswitchanalyzer" title="statistical identification of isoform switching"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">IsoformSwitchAnalyzeR</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=sleuth" title="Differential expression analysis"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Sleuth</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=trinity_stats" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Trinity Stats</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=cmsearch_deoverlap" title="removes lower scoring overlaps from cmsearch results"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CMsearch deoverlap</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=psiclass" title="reference-based transcriptome assembler"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PsiCLASS</button></a>
@@ -1464,15 +1495,7 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=hicup2juicer" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Hicup to juicer converter</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=cooler_zoomify" title="Generate a multi-resolution cooler file by coarsening"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Cooler zoomify</button></a>
 <h3 id="phylogenetics">Phylogenetics</h3>
-<a href="https://usegalaxy.eu/root?tool_id=ete_gene_csv_finder" title="from a genetree using the ETE Toolkit"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Gene Copy Number Finder</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ete_genetree_splitter" title="from a genetree using the ETE Toolkit"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ETE GeneTree splitter</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ete_homology_classifier" title="from a genetree using the ETE Toolkit"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Homology Classifier and Filter</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ete_init_taxdb" title="generates the ETE sqlite DB from the NCBI taxdump.tar.gz"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ETE taxa DB generator</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ete_lineage_generator" title="from a list of species/taxids using the ETE Toolkit"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ETE lineage generator</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ete3_mod" title="manipulates tree topology by rooting, pruning or sorting branches"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ETE mod</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ete_species_tree_generator" title="from a list of species using the ETE Toolkit"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ETE species tree generator</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=t_coffee" title="multiple sequence alignment"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">T-Coffee</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=gafa" title="generates an SQLite database that can be visualised with Aequatus"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Gene Align and Family Aggregator</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=read2tree" title="Infer a species tree from sequencing reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Read2Tree</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=hyphy_prime" title="Property Informed Models of Evolution"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">HyPhy-PRIME</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=hyphy_busted" title="Branch-site Unrestricted Statistical Test for Episodic Diversification"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">HyPhy-BUSTED</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=hyphy_bgm" title="- Detecting coevolving sites via Bayesian graphical models"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">HyPhy-BGM</button></a>
@@ -1488,18 +1511,27 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=sarscov2formatter" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">sarscov2formatter</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=raxml" title="Maximum Likelihood based inference of large phylogenetic trees"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RAxML</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=gstf_preparation" title="converts data for the workflow"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GeneSeqToFamily preparation</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=iframe" title="opens an IFrame to Apollo"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Annotate</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=create_account" title="with Apollo"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Register Account</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=list_organism" title="in Apollo"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">List Organisms</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=phyml" title="Phylogeny software based on the maximum-likelihood method"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PhyML</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=sarscov2summary" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">sarscov2summary</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=squirrel_phylo" title="Phylogenetic and APOBEC3 analysis of MPXV (Mpox virus)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Squirrel Phylo</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=squirrel_qc" title="QC of MPXV (Mpox virus) sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Squirrel QC</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ete_treeviewer" title="visualize a phylogenetic tree"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ETE tree viewer</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=blast_parser" title="Convert 12- or 24-column BLAST output into 3-column hcluster_sg input"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BLAST parser</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ete_gene_csv_finder" title="from a genetree using the ETE Toolkit"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Gene Copy Number Finder</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=hcluster_sg_parser" title="converts hcluster_sg 3-column output into lists of IDs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hcluster_sg parser</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ete_lineage_generator" title="from a list of species/taxids using the ETE Toolkit"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ETE lineage generator</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ete_species_tree_generator" title="from a list of species using the ETE Toolkit"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ETE species tree generator</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ete_genetree_splitter" title="from a genetree using the ETE Toolkit"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ETE GeneTree splitter</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ete_homology_classifier" title="from a genetree using the ETE Toolkit"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Homology Classifier and Filter</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ete_init_taxdb" title="generates the ETE sqlite DB from the NCBI taxdump.tar.gz"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ETE taxa DB generator</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ete3_mod" title="manipulates tree topology by rooting, pruning or sorting branches"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ETE mod</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=treebest_best" title="Generate a phylogenetic tree using CDS alignment and species tree"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">TreeBeST best</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=species_tree_generator" title="from a list of species using the ETE Toolkit"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Species tree generator</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=gafa" title="generates an SQLite database that can be visualised with Aequatus"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Gene Align and Family Aggregator</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=treebest_best_wrapper" title="Generate a phylogenetic tree using CDS alignment and species tree"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">TreeBeST best</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=fasta_header_converter" title="to append species information"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FASTA header converter</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=t_coffee" title="multiple sequence alignment"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">T-Coffee</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=hcluster_sg" title="Hierarchically clustering on a sparse graph"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hcluster_sg</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=blast_parser" title="Convert 12- or 24-column BLAST output into 3-column hcluster_sg input"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BLAST parser</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=nextalign" title="Viral genome sequence alignment"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NextAlign</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=pangolin" title="Phylogenetic Assignment of Outbreak Lineages"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Pangolin</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=nextclade" title="Viral genome clade assignment, mutation calling, and sequence quality checks"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Nextclade</button></a>
@@ -1523,6 +1555,15 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=hybpiper" title="Analyse targeted sequence capture data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">HybPiper</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=pacu_map" title="Map ONT / Illumina reads to a reference genome for PACU"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PACU - mapping</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=pacu_snp" title="whole genome sequencing based phylogeny of Illumina and ONT R9/R10 data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PACU</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=squirrel_phylo" title="Phylogenetic and APOBEC3 analysis of MPXV (Mpox virus)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Squirrel Phylo</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=squirrel_qc" title="QC of MPXV (Mpox virus) sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Squirrel QC</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ete_treeviewer" title="visualize a phylogenetic tree"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ETE tree viewer</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=mrbayes" title="with options and commands"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MrBayes</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=fastreer_dist2tree" title="Newick tree from distance matrix"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">DIST2TREE</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=fastreer_fasta2dist" title="Compute D2S distance matrix from FASTA file(s)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FASTA2DIST</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=fastreer_vcf2dist" title="Cosine distance matrix from VCF files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VCF2DIST</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=fastreer_vcf2tree" title="Newick tree from VCF files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VCF2TREE</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=raxmlng" title="Maximum Likelihood based inference of large phylogenetic trees"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RAxML-NG</button></a>
 <h3 id="phenotypeassociation">Phenotype Association</h3>
 <a href="https://usegalaxy.eu/root?tool_id=vcf2pgSnp" title="Convert from VCF to pgSnp format"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VCF to pgSnp</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=hgv_snpFreq" title="significant SNPs in case-control data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">snpFreq</button></a>
@@ -1530,6 +1571,8 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=hgv_hilbertvis" title="visualization of genomic data with the Hilbert curve"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">HVIS</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=dividePgSnp" title="into columns"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Separate pgSnp alleles</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ctdBatch_1" title="analysis of chemicals, diseases, or genes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CTD</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=gemma" title="Run association tests and kinship analysis with GEMMA"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GEMMA Analysis</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=quality_control" title="Run quality control on genotype data for GWAS analysis."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Quality control for GWAS analysis</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=hgv_linkToGProfile" title="tools for functional profiling of gene lists"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">g:Profiler</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=hgv_david" title="functional annotation for a list of genes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">DAVID</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=hgv_ldtools" title="linkage disequilibrium and tag SNPs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">LD</button></a>
@@ -1539,18 +1582,9 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=hgv_lps" title="LASSO-Patternsearch algorithm"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">LPS</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=master2pgSnp" title="Convert from MasterVar to pgSnp format"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MasterVar to pgSnp</button></a>
 <h3 id="single-cell">Single-cell</h3>
-<a href="https://usegalaxy.eu/root?tool_id=vpt_extract" title="image patches"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Vizgen VPT - Extract</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=vpt_segment" title="cells and refine MERSCOPE experiments"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Vizgen VPT - Segment</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bellavista_prepare" title="Prepare large images for bellavista visualizer"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Bellavista</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=anndata_import" title="from different formats"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Import Anndata</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=scanpy_inspect" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Scanpy Inspect and manipulate</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=drug2cell" title="Collection of utility functions for gene group activity evaluation in scanpy"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">drug2cell</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=mudata_import_export" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MuData import and export</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=preprocess_muon" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">muon filter and  normalize</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=spacexr_cside" title="Cell type-specific differential expression with C-SIDE"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CSIDE</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=anndata_manipulate" title="object"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Manipulate AnnData</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=anndata_export" title="matrix and annotations"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Export AnnData</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=music_manipulate_eset" title="Manipulate ExpressionSet objects by a variety of attributes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Manipulate Expression Set Object</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=anndata_manipulate" title="object"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Manipulate AnnData</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=anndata_inspect" title="object"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Inspect AnnData</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=modify_loom" title="Manipulate, export and import loom data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Loom operations</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=dropletutils" title="Utilities for handling droplet-based single-cell RNA-seq data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">DropletUtils</button></a>
@@ -1558,12 +1592,12 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=dropletutils_empty_drops" title="Distinguish between droplets containing cells and ambient RNA in a droplet-based single-cell RNA sequencing experiment."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">DropletUtils emptyDrops</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=alevin" title="Quantification and analysis of 3-prime tagged-end single-cell sequencing data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Alevin</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=scanpy_filter" title="mark and subsample"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Scanpy filter</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=scanpy_inspect" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Scanpy Inspect and manipulate</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=scanpy_normalize" title="and impute"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Scanpy normalize</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=scanpy_plot" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Scanpy plot</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=scanpy_remove_confounders" title="with scanpy"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Scanpy remove confounders</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ip_slice_image" title="into smaller patches"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Slice Image</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=scanpy_cluster_reduce_dimension" title="and infer trajectories"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Scanpy cluster, embed</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=scanpy_parameter_iterator" title="produce an iteration over a defined parameter"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Scanpy ParameterIterator</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=scater_plot_tsne" title="of two components"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Scater: t-SNE plot</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=scater_plot_pca" title="cell-level reduced dimension of a normalised SCE"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Scater: PCA plot</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=scater_plot_exprs_freq" title="Plot the frequency of expression against the mean expression level for SCE"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Scater: plot expression frequency</button></a>
@@ -1577,6 +1611,7 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=raceid_trajectory" title="generates lineage from prior clustering"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Lineage computation using StemID</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=raceid_inspecttrajectory" title="inspects branches of a lineage tree"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Lineage Branch Analysis using StemID</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=music_deconvolution" title="estimate cell type proportions in bulk RNA-seq data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MuSiC Deconvolution</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=music_manipulate_eset" title="Manipulate ExpressionSet objects by a variety of attributes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Manipulate Expression Set Object</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=music_construct_eset" title="Create an ExpressionSet object from tabular and textual data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Construct Expression Set Object</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=music_inspect_eset" title="Inspect an ExpressionSet object by a variety of attributes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Inspect Expression Set Object</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=music_compare" title="estimate and compare cell type proportions in multiple sets of bulk RNA-seq data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MuSiC Compare</button></a>
@@ -1584,14 +1619,6 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=cite_seq_count" title="Count CMO/HTO"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CITE-seq-Count</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=sinto_barcode" title="add cell barcodes to FASTQ read names"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Sinto barcode</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=sinto_fragments" title="Create an ATAC-seq fragment file from a BAM file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Sinto fragments</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=episcanpy_build_matrix" title="with EpiScanpy"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Build count matrix</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=episcanpy_preprocess" title="with EpiScanpy"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">scATAC-seq Preprocessing</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=episcanpy_cluster_embed" title="with EpiScanpy"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Cluster, embed and annotate</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=spacexr_rctd" title="Cell type identification with RCTD"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RCTD</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=plot_muon" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">muon plot</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=cluster_analyze_embed_muon" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">muon Cluster, analyze, and embed multimodal data</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=anndata2ri" title="Convert between Anndata and SingCellExperiment objects"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">anndata2ri</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=quantification" title="a module for single-cell data extraction"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MCQUANT</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=velocyto_cli" title="pre-process data for the analysis of RNA velocity"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">velocyto CLI</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=baredsc_1d" title="Compute distribution for a single gene"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">baredSC 1d</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=baredsc_2d" title="Compute distribution for a pair of genes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">baredSC 2d</button></a>
@@ -1606,6 +1633,18 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=cosg" title="Cell marker gene identification"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">COSG</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=spapros_selection" title="of marker genes with spapros"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Selection</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=spapros_evaluation" title="of marker genes with spapros"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Evaluation</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=spacexr_rctd" title="Cell type identification with RCTD"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RCTD</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=spacexr_cside" title="Cell type-specific differential expression with C-SIDE"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CSIDE</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=mudata_import_export" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MuData import and export</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=preprocess_muon" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">muon filter and  normalize</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=plot_muon" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">muon plot</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cluster_analyze_embed_muon" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">muon Cluster, analyze, and embed multimodal data</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=anndata2ri" title="Convert between Anndata and SingCellExperiment objects"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">anndata2ri</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=drug2cell" title="Collection of utility functions for gene group activity evaluation in scanpy"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">drug2cell</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bellavista_prepare" title="Prepare large images for bellavista visualizer"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Bellavista</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=vpt_segment" title="cells and refine MERSCOPE experiments"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Vizgen VPT - Segment</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=vpt_extract" title="image patches"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Vizgen VPT - Extract</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=quantification" title="a module for single-cell data extraction"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MCQUANT</button></a>
 <h3 id="spatialomics">Spatial Omics</h3>
 <a href="https://usegalaxy.eu/root?tool_id=mesmer" title="with Mesmer"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Perform segmentation of multiplexed tissue data</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=basic_illumination" title="ImageJ BaSiC shading correction for use with Ashlar"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BaSiC Illumination</button></a>
@@ -1645,7 +1684,6 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=picard_AddCommentsToBam" title="add comments to BAM dataset"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">AddCommentsToBam</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=picard_CollectInsertSizeMetrics" title="plots distribution of insert sizes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CollectInsertSizeMetrics</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=picard_ReplaceSamHeader" title="replace header in a SAM/BAM dataset"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ReplaceSamHeader</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=picard_artifact_metrics" title="Collect metrics to quantify single-base sequencing artifacts"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Picard Collect Sequencing Artifact Metrics</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=PicardASMetrics" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SAM/BAM Alignment Summary Metrics</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=picard_ARRG" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Add or Replace Groups</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=picard_BamIndexStats" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BAM Index Statistics</button></a>
@@ -1653,6 +1691,7 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=rgEstLibComp" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Estimate Library Complexity</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=rgPicFixMate" title="for paired data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Paired Read Mate Fixer</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=picard_CollectHsMetrics" title="compute metrics about datasets generated through hybrid-selection (e.g. exome)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CollectHsMetrics</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=picard_artifact_metrics" title="Collect metrics to quantify single-base sequencing artifacts"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Picard Collect Sequencing Artifact Metrics</button></a>
 <h3 id="deeptools">deepTools</h3>
 <a href="https://usegalaxy.eu/root?tool_id=deeptools_bam_compare" title="normalizes and compares two BAM or CRAM files to obtain the ratio, log2ratio or difference between them"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bamCompare</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=deeptools_bam_coverage" title="generates a coverage bigWig file from a given BAM or CRAM file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bamCoverage</button></a>
@@ -1805,13 +1844,7 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=emboss_needleall" title="Many-to-many Needleman-Wunsch global alignment"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">EMBOSS: needleall</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=emboss_needle" title="Needleman-Wunsch global alignment"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">EMBOSS: needle</button></a>
 <h3 id="ncbiblast">NCBI Blast</h3>
-<a href="https://usegalaxy.eu/root?tool_id=bg_diamond_makedb" title="Build database from a FASTA file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Diamond makedb</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bg_diamond_view" title="generate formatted output from DAA files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Diamond view</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=blastxml_to_top_descr" title="Make a table from BLAST output"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BLAST top hit descriptions</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bg_diamond" title="alignment tool for short sequences against a protein database"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Diamond</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bbtools_callvariants" title="in aligned Bam files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BBTools: call variants</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=blastxml_to_tabular" title="Convert BLAST XML output to tabular"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BLAST XML to tabular</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=get_species_taxids" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NCBI get species taxids</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ncbi_blastdbcmd_info" title="Show BLAST database information from blastdbcmd"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NCBI BLAST+ database info</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ncbi_blastdbcmd_wrapper" title="Extract sequence(s) from BLAST database"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NCBI BLAST+ blastdbcmd entry(s)</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ncbi_blastn_wrapper" title="Search nucleotide database with nucleotide query sequence(s)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NCBI BLAST+ blastn</button></a>
@@ -1826,39 +1859,44 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=ncbi_segmasker_wrapper" title="low-complexity regions in protein sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NCBI BLAST+ segmasker</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ncbi_tblastn_wrapper" title="Search translated nucleotide database with protein query sequence(s)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NCBI BLAST+ tblastn</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ncbi_tblastx_wrapper" title="Search translated nucleotide database with translated nucleotide query sequence(s)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NCBI BLAST+ tblastx</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=magicblast" title="against a whole genome or transcriptome"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Magic-BLAST: map large RNA or DNA sequences</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bg_diamond_view" title="generate formatted output from DAA files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Diamond view</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bg_diamond" title="align short sequences against a protein database"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Diamond</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bg_diamond_makedb" title="build database from a FASTA file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Diamond makedb</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=blast_reciprocal_best_hits" title="from two FASTA files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BLAST Reciprocal Best Hits (RBH)</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=blastxml_to_top_descr" title="Make a table from BLAST output"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BLAST top hit descriptions</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bbtools_callvariants" title="in aligned Bam files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BBTools: call variants</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=get_species_taxids" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NCBI get species taxids</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=magicblast" title="against a whole genome or transcriptome"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Magic-BLAST: map large RNA or DNA sequences</button></a>
 <h3 id="hicexplorer">HiCExplorer</h3>
-<a href="https://usegalaxy.eu/root?tool_id=hicexplorer_hicvalidatelocations" title="validate detected loops with protein peaks."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hicValidateLocations</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=hicexplorer_hicsummatrices" title="combine Hi-C matrices of the same size"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hicSumMatrices</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=hicexplorer_hicplotsvl" title="plots the relation of short vs long range contacts"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hicPlotSVL</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=hicexplorer_hicplotdistvscounts" title="compute distance vs Hi-C counts plot per chromosome"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hicPlotDistVsCounts</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=hicexplorer_hicmergematrixbins" title="merge adjacent bins from a Hi-C contact matrix to reduce its resolution"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hicMergeMatrixBins</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=hicexplorer_hichyperoptDetectLoops" title="optimizes parameters for hicDetectLoops"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hicHyperoptDetectLoops</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=hicexplorer_hicfindtads" title="identify TAD boundaries by computing the degree of separation of each Hi-C matrix bin"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hicFindTADs</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=hicexplorer_hicconvertformat" title="Convert between different file formats"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hicConvertFormat</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=hicexplorer_hicbuildmatrix" title="create a contact matrix"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hicBuildMatrix</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=hicexplorer_hicaggregatecontacts" title="allow plotting of aggregated Hi-C contacts between regions specified in a file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hicAggregateContacts</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=hicexplorer_chicdifferentialtest" title="computes differential interactions of viewpoints"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">chicDifferentialTest</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=schicexplorer_schicqualitycontrol" title="quality control for single-cell Hi-C interaction matrices"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">scHicQualityControl</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=hicexplorer_chicplotviewpoint" title="creates plots for viewpoints"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">chicPlotViewpoint</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=hicexplorer_chicdifferentialtest" title="computes differential interactions of viewpoints"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">chicDifferentialTest</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=hicexplorer_chicaggregatestatistic" title="computes with a target file the to be tested regions for chicDifferentialTest"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">chicAggregateStatistic</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=hicexplorer_chicsignificantinteractions" title="computes viewpoints with the given reference points and a background model"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">chicSignificantInteractions</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=hicexplorer_chicviewpoint" title="computes viewpoints with the given reference points and a background model."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">chicViewpoint</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=hicexplorer_hicplotviewpoint" title="plot interactions around a viewpoint"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hicPlotViewpoint</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=hicexplorer_hicplotsvl" title="plots the relation of short vs long range contacts"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hicPlotSVL</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=hicexplorer_hicplotmatrix" title="plot a Hi-C contact matrix heatmap"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hicPlotMatrix</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=hicexplorer_hicplotdistvscounts" title="compute distance vs Hi-C counts plot per chromosome"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hicPlotDistVsCounts</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=hicexplorer_hicplotaverageregions" title="plot the average regions from hicAverageRegions"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hicPlotAverageRegions</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=hicexplorer_hicpca" title="compute the principal components for A / B compartment analysis"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hicPCA</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=hicexplorer_hicfindtads" title="identify TAD boundaries by computing the degree of separation of each Hi-C matrix bin"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hicFindTADs</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=hicexplorer_hicvalidatelocations" title="validate detected loops with protein peaks."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hicValidateLocations</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=hicexplorer_hicmergeloops" title="merge detected loops of different resolutions."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hicMergeLoops</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=hicexplorer_hicdetectloops" title="searches for enriched regions"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hicDetectLoops</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=hicexplorer_hiccorrelate" title="compute pairwise correlations between multiple Hi-C contact matrices"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hicCorrelate</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=hicexplorer_hiccompartmentspolarization" title="compute pairwise correlations between multiple Hi-C contact matrices"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hicCompartmentalization</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=hicexplorer_hiccomparematrices" title="normalize and compare two Hi-C contact matrices"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hicCompareMatrices</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=hicexplorer_hicaverageregions" title="sums Hi-C contacts around given reference points and computes their average."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hicAverageRegions</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=hicexplorer_hicaggregatecontacts" title="allow plotting of aggregated Hi-C contacts between regions specified in a file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hicAggregateContacts</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=hicexplorer_hiccorrectmatrix" title="run a Hi-C matrix correction algorithm"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hicCorrectMatrix</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=hicexplorer_hicnormalize" title="normalizes a matrix to norm range or smallest read count"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hicNormalize</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=hicexplorer_hictransform" title="transform a matrix to obs/exp, pearson and covariance matrices"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hicTransform</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=hicexplorer_hicsummatrices" title="combine Hi-C matrices of the same size"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hicSumMatrices</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=hicexplorer_hicmergematrixbins" title="merge adjacent bins from a Hi-C contact matrix to reduce its resolution"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hicMergeMatrixBins</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=hicexplorer_hicconvertformat" title="Convert between different file formats"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hicConvertFormat</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=hicexplorer_hicadjustmatrix" title="adjust the shape of a Hi-C matrix"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hicAdjustMatrix</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=hicexplorer_hicbuildmatrix" title="create a contact matrix"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hicBuildMatrix</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=hicexplorer_hicfindrestrictionsites" title="identify restriction enzyme sites"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hicFindRestSite</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=hicexplorer_hicinfo" title="get information about the content of a Hi-C matrix"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hicInfo</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=hicexplorer_hicquickqc" title="get a first quality estimate of Hi-C data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hicQuickQC</button></a>
@@ -1880,10 +1918,11 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=schicexplorer_schiccluster" title="clusters single-cell Hi-C interaction matrices on the raw data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">scHicCluster</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=schicexplorer_schicadjustmatrix" title="clusters single-cell Hi-C interaction matrices on the raw data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">scHicAdjustMatrix</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=hicexplorer_hicplottads" title="plot Hi-C contact matrices heatmaps alongside other data tracks"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hicPlotTADs</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=hicexplorer_chicexportdata" title="exports data of hdf to txt based files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">chicExportData</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=hicexplorer_hichyperoptDetectLoops" title="optimizes parameters for hicDetectLoops"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hicHyperoptDetectLoops</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=hicexplorer_hicdifferentialtad" title="searches for differential TADs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hicDifferentialTAD</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=hicexplorer_hicinterintratad" title="computes the ratio of inter TAD-scores vs. intra TADs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hicInterIntraTAD</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=hicexplorer_hicmergedomains" title="Merges TAD domains"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hicMergeDomains</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=hicexplorer_chicexportdata" title="exports data of hdf to txt based files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">chicExportData</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=hicexplorer_hicinterintratad" title="computes the ratio of inter TAD-scores vs. intra TADs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hicInterIntraTAD</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=hicexplorer_hictadclassifier" title="TAD detection based on ML models"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hicTADClassifier</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=hicexplorer_hictraintadclassifier" title="train a TAD detection ML model"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">hicTrainTADClassifier</button></a>
 <h3 id="rad-seq">RAD-seq</h3>
@@ -1913,6 +1952,9 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=stacks_refmap" title="the Stacks pipeline with a reference genome (ref_map.pl)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Stacks: reference map</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=stacks_rxstacks" title="make corrections to genotype and haplotype calls"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Stacks: rxstacks</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=stacks_pstacks" title="find stacks from short reads mapped to a reference genome"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Stacks: pstacks</button></a>
+<h3 id="digitalhumanities">Digital Humanities</h3>
+<a href="https://usegalaxy.eu/root?tool_id=spacy_nlp" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">spaCy NLP Annotators</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=stanford_corenlp" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Stanford CoreNLP Annotators (Multi-language)</button></a>
 <h3 id="graphclust">GraphClust</h3>
 <a href="https://usegalaxy.eu/root?tool_id=graphicsmagick_image_convert" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Image Converter</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=NSPDK_candidateClust" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NSPDK_candidateClusters</button></a>
@@ -1948,32 +1990,14 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=mimodd_sort" title="takes a SAM/BAM dataset and generates a coordinate/name-sorted copy"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MiModD Sort</button></a>
 <hr/><h2 id="metagenomics">Metagenomics</h2>
 <h3 id="metagenomicanalysis">Metagenomic Analysis</h3>
-<a href="https://usegalaxy.eu/root?tool_id=checkm_lineage_set" title="Infer lineage-specific marker sets for each bin"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CheckM lineage_set</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=virannot_otu" title="create viral OTUs based on RPS and Blast annotations"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">virAnnot OTU</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=mmuphin" title="Performing meta-analyses of microbiome studies"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">mmuphin</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=drep_compare" title="compare a list of genomes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">dRep compare</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=profile2cami" title="Convert metagenomic profile table to CAMI format"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Profile2CAMI</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=name2taxid" title="Convert taxon names to NCBI Taxids"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Name2taxid</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=kaiju_kaiju2krona" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">kaiju2krona</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=vibrant" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VIBRANT</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=kmer2stats" title="A tool that computes kmer alpha diversity metrics and other statistics"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Kmer2Stats</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=kaiju_kaiju2table" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">kaiju2table</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=semibin_train" title="the semi-supervised deep learning model"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SemiBin: Train</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=binette" title="Binning refinement tool"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Binette</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=phyloseq_plot_ordination" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Phyloseq: plot ordination</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=phyloseq_plot_bar" title="Generate bar charts from a phyloseq object"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Phyloseq: Bar Chart</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=metaphlan" title="to profile the composition of microbial communities"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MetaPhlAn</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=dada2_assignTaxonomyAddspecies" title="Learn Error rates"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">dada2: assignTaxonomy and addSpecies</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=phyloseq_plot_richness" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Phyloseq: plot alpha diverstiy measure</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=phyloseq_add_rank_names" title="Add taxonomy rank names to a phyloseq object"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Add Rank Names to Phyloseq Object</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=biobox_add_taxid" title="Add taxid output from BAT or GTDB to biobox binning data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Biobox add taxid</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=phyloseq_from_dada2" title="from dada2 sequence and taxonomy tables"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Create phyloseq object</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=fairy_sketch" title="sketching of k-mers for coverage into a hashtable"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Fairy sketch</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=decontam" title="Identification and removal of contaminants"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Decontam</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=comebin_bam" title="COMEBin utility script to generate BAM files using modified MetaWRAP"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Generate BAM file for COMEBin</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=gtdbtk_classify_wf" title="by placement in GTDB reference tree"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GTDB-Tk Classify genomes</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=vrhyme" title="Dereplication and Binning Virus Genomes from Metagenomes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">vRhyme</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=kraken2" title="assign taxonomic labels to sequencing reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Kraken2</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=dada2_makeSequenceTable" title="construct a sequence table (analogous to OTU table)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">dada2: makeSequenceTable</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=dada2_plotQualityProfile" title="plot a visual summary of the quality scores"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">dada2: plotQualityProfile</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=dada2_mergePairs" title="Merge denoised forward and reverse reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">dada2: mergePairs</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=dada2_assignTaxonomyAddspecies" title="Learn Error rates"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">dada2: assignTaxonomy and addSpecies</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=dada2_plotComplexity" title="Plot sequence complexity profile"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">dada2: plotComplexity</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=dada2_learnErrors" title="Learn Error rates"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">dada2: learnErrors</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=dada2_dada" title="Remove sequencing errors"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">dada2: dada</button></a>
@@ -1986,12 +2010,13 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=vsearch_search" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VSearch search</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=last_al" title="finds local alignments between query sequences, and reference sequences."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">LASTal</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=drep_dereplicate" title="De-replicate a list of genomes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">dRep dereplicate</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=drep_compare" title="compare a list of genomes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">dRep compare</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=last_db" title="prepares sequences for subsequent comparison and alignment using lastal."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">LASTdb</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=last_split" title="finds 'split alignments' (typically for DNA) or 'spliced alignments' (typically for RNA)."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">LAST-split</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=last_maf_convert" title="read MAF-format alignments and write them in another format."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MAF-convert</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=mash_screen" title="determines how well query sequences are contained within a pool of sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">mash screen</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=mash_screen" title="Determine sequence conservation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">mash screen</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=metagene_annotator" title="gene-finding program for prokaryote and phage (used by sixgill)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MetaGeneAnnotator</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=mash_sketch" title="Create a reduced representation of a sequence or set of sequences, based on min-hashes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">mash sketch</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=mash_sketch" title="Create a reduced sequence representation based on min-hashes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">mash sketch</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=sixgill_merge" title="metapeptide databases"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">sixgill merge</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=sixgill_filter" title="a metapeptide database"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">sixgill filter</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=sixgill_build" title="a metapeptide database from metagenome fastq files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">sixgill build</button></a>
@@ -2050,6 +2075,7 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=humann_split_stratified_table" title="into 2 tables (one stratified and one unstratified)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Split a HUMAnN table</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=humann_split_table" title="a merged HUMAnN table"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Split</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=humann_unpack_pathways" title="to show the genes for each"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Unpack pathway abundances</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=metaphlan" title="to profile the composition of microbial communities"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MetaPhlAn</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=extract_metaphlan_database" title="from the MetaPhlAn database"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Extract the marker sequences and metadata</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=customize_metaphlan_database" title="from the MetaPhlAn database"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Customize the marker sequences and metadata</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=lotus2" title="fast OTU processing pipeline"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">LotuS2</button></a>
@@ -2069,6 +2095,9 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=metabat2_jgi_summarize_bam_contig_depths" title="for MetaBAT2"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Calculate contig depths</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=metabat2" title="metagenome binning"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MetaBAT2</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=bin_refiner" title="refines metagenome bins"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Binning refiner</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=phyloseq_from_dada2" title="from dada2 sequence and taxonomy tables"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Create phyloseq object</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=phyloseq_plot_ordination" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Phyloseq: plot ordination</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=phyloseq_plot_richness" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Phyloseq: plot alpha diverstiy measure</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=concoct" title="for metagenome binning"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CONCOCT</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=concoct_coverage_table" title="for CONCOCT"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CONCOCT: Generate the input coverage table</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=concoct_cut_up_fasta" title="in non-overlapping or overlapping parts of equal length"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CONCOCT: Cut up contigs</button></a>
@@ -2093,6 +2122,7 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=checkm_qa" title="Assess bins for contamination and completeness"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CheckM qa</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=checkm_taxon_set" title="Generate taxonomic-specific marker set"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CheckM taxon_set</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=checkm_plot" title="for assessing the quality of genome bins"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CheckM plot</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=checkm_lineage_set" title="Infer lineage-specific marker sets for each bin"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CheckM lineage_set</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=srst2" title="Short Read Sequence Typing for Bacterial Pathogens"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SRST2</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=kraken_biom" title="Create BIOM-format tables from kraken output"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Kraken-biom</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=vapor" title="Classify Influenza samples from short reads sequence data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VAPOR</button></a>
@@ -2100,6 +2130,7 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=polypolish" title="Short-read polishing of long-read bacterial genome assemblies"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Polypolish</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=semibin_generate_cannot_links" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SemiBin: Contig annotations</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=semibin" title="for Semi-supervised Metagenomic Binning"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SemiBin</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=semibin_train" title="the semi-supervised deep learning model"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SemiBin: Train</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=semibin_generate_sequence_features" title="(kmer and abundance) as training data for semi-supervised deep learning model training"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SemiBin: Generate sequence features</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=semibin_bin" title="into bins"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SemiBin: Group the contigs</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=semibin_concatenate_fasta" title="for multi-sample binning"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SemiBin: Concatenate fasta files</button></a>
@@ -2134,40 +2165,71 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=krakentools_combine_kreports" title="into a combined report file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Krakentools: Combine multiple Kraken reports</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=krakentools_extract_kraken_reads" title="Extract reads that were classified by the Kraken family at specified taxonomic IDs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Krakentools: Extract Kraken Reads By ID</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=dada2_seqCounts" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">dada2: sequence counts</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=dada2_primerCheck" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">dada2: primer check</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=phyloseq_from_biom" title="from a BIOM file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Create phyloseq object</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=fairy_cov" title="Create coverage file for specific binners"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Fairy coverage</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=checkm2" title="Rapid assessment of genome bin quality using machine learning"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">checkm2</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=metawrapmg_binning" title="metagenome binning pipeline"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MetaWRAP</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=gtdbtk_classify_wf" title="by placement in GTDB reference tree"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GTDB-Tk Classify genomes</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=qiime2_dbotu_q2" title="QIIME 2 plugin for distribution-based clustering"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 dbOTU</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ampvis2_export_otu" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ampvis2 export otu</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=kaiju_addtaxonnames" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">kaiju-addTaxonNames</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=phyloseq_tax_glom" title="Aggregates a Phyloseq object at a specified taxonomic rank"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Phyloseq Taxonomic Agglomeration</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=kaiju_mergeoutputs" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">kaiju-mergeOutputs</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=kaiju_kaiju" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">kaiju</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=iphop_predict" title="host of input bacteriophage/archaeal virus genomes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">iPHoP predict</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=virannot_blast2tsv" title="convert XML blast results to tabular file with taxonomic informations"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">virAnnot Blast2tsv</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=vrhyme" title="Dereplication and Binning Virus Genomes from Metagenomes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">vRhyme</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=virAnnot_rps2tsv" title="Convert xml rpstblast results to tab file with taxonomic informations"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">virAnnot Rps2tsv</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=sylph_query" title="compare metagenome similarity to a reference genome"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">sylph query</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=sylph_profile" title="Profile a metagenome including taxonomic and sequence abundances"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">sylph profile</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=genomad_end_to_end" title="identify virus and plasmid genomes from nucleotide sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">geNomad</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=combine_metaphlan_humann" title="to relate genus/species abundances and gene families/pathways abundances"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Combine MetaPhlAn and HUMAnN outputs</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=mapseq" title="sequence read classification designed to assign taxonomy and OTU classifications"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MAPseq</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=seqsero2" title="Salmonella serotype prediction"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SeqSero2</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=bigscape" title="Construct sequence similarity networks of BGCs and group them into GCF"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BiG-SCAPE</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=phyloseq_from_biom" title="from a BIOM file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Create phyloseq object</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=virannot_blast2tsv" title="convert XML blast results to tabular file with taxonomic informations"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">virAnnot Blast2tsv</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=virannot_otu" title="create viral OTUs based on RPS and Blast annotations"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">virAnnot OTU</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=virAnnot_rps2tsv" title="Convert xml rpstblast results to tab file with taxonomic informations"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">virAnnot Rps2tsv</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=sirius_csifingerid" title="is used to identify metabolites using single and        tandem mass spectrometry"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SIRIUS-CSI:FingerID</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=metawrapmg_binning" title="metagenome binning"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MetaWRAP</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=qiime2__dada2__denoise_ccs" title="Denoise and dereplicate single-end Pacbio CCS"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 dada2 denoise-ccs</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=cami_amber" title="Evaluation package for MAGs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CAMI AMBER</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=taxpasta" title="standardise taxonomic profiles"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">taxpasta</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=genomad_end_to_end" title="identify virus and plasmid genomes from nucleotide sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">geNomad</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=mg_toolkit_original_metadata" title="Download original metadata for a study"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Metagenomics toolkit Original Metadata</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=mg_toolkit_bulk_download" title="Download result files in bulks for an entire study"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Metagenomics toolkit Bulk Download</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=name2taxid" title="Convert taxon names to NCBI Taxids"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Name2taxid</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=gtdb_to_taxdump" title="Map taxonomic classifications between the NCBI and GTDB taxonomies"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NCBI-GTDB map</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=biobox_add_taxid" title="Add taxid output from BAT or GTDB to biobox binning data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Biobox add taxid</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=maaslin3" title="Microbiome Multivariable Association with Linear Models"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MaAsLin3</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=mereg_mOTUs_tables" title="Merge mOTUs aboundance or count tables"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Merge</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=motus_profiler" title="performs taxonomic profiling of metagenomics and metatrancriptomics samples"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">mOTUs_profiler</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=tiara" title="Deep-learning-based approach for identification of eukaryotic sequences in the metagenomic data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">tiara</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=vibrant" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VIBRANT</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=virsorter" title="identify DNA and RNA virus"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VirSorter</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=profile2cami" title="Convert metagenomic profile table to CAMI format"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Profile2CAMI</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=decontam" title="Identification and removal of contaminants"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Decontam</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=dada2_primerCheck" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">dada2: primer check</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=phyloseq_plot_bar" title="Generate bar charts from a phyloseq object"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Phyloseq: Bar Chart</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=phyloseq_add_rank_names" title="Add taxonomy rank names to a phyloseq object"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Add Rank Names to Phyloseq Object</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=fairy_cov" title="Create coverage file for specific binners"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Fairy coverage</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=fairy_sketch" title="sketching of k-mers for coverage into a hashtable"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Fairy sketch</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=binette" title="Binning refinement tool"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Binette</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=checkm2" title="Rapid assessment of genome bin quality using machine learning"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">checkm2</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=mmuphin" title="Performing meta-analyses of microbiome studies"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">mmuphin</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2_dbotu_q2" title="QIIME 2 plugin for distribution-based clustering"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 dbOTU</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ampvis2_export_otu" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ampvis2 export otu</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=phyloseq_tax_glom" title="Aggregates a Phyloseq object at a specified taxonomic rank"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Phyloseq Taxonomic Agglomeration</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=kmer2stats" title="A tool that computes kmer alpha diversity metrics and other statistics"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Kmer2Stats</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=kaiju_addtaxonnames" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">kaiju-addTaxonNames</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=kaiju_kaiju2table" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">kaiju2table</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=kaiju_kaiju2krona" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">kaiju2krona</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=kaiju_mergeoutputs" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">kaiju-mergeOutputs</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=kaiju_kaiju" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">kaiju</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=iphop_predict" title="host of input bacteriophage/archaeal virus genomes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">iPHoP predict</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=sylph_query" title="compare metagenome similarity to a reference genome"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">sylph query</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=sylph_profile" title="Profile a metagenome including taxonomic and sequence abundances"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">sylph profile</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=comebin" title="Binning of metagenomic contigs using COntrastive Multi-viEw representation learning"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">COMEBin</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=micro_decon" title="removing contamination from metabarcoding"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">micro_decon</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=pimento_are_there_primers" title="Checks for the presence of primers in input reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PIMENTO Are there primers?</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=pimento_auto" title="Infers primers by predicting optimal cutoff points from read conservation patterns"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PIMENTO Primer cutoff prediction</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=pimento_choose_primer_cutoff" title="Selects optimal primer cutoff and generates final inferred primer sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PIMENTO Choose primer cutoff</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=pimento_find_cutoffs" title="Identifies potential primer cutoff points from base-conservation vectors"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PIMENTO Find cutoffs</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=pimento_gen_bcv" title="for primer fastq files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PIMENTO Generate base-conservation vector(s)</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=pimento_std" title="Finds best-matching primers in reads using a fuzzy search against a standard primer library"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PIMENTO Standard primer matching</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=metasbt_index" title="genomes with Sequence Bloom Trees or update an existing database"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">index</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=metasbt_profile" title="genomes with MetaSBT to infer their taxonomic"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">profile</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=phi_toolkit_report" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PHI toolkit report</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=defense_finder" title="systematically detect known anti-phage systems"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">DefenseFinder</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=abims_xcms_xcmsSet" title="Chromatographic peak detection"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">xcms findChromPeaks (xcmsSet)</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=mash_paste" title="Create a single sketch file from multiple sketch files."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">mash paste</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=mash_dist" title="Estimate distance between query sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">mash dist</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=metawrapmg_bin_refinement" title="metagenome bin refinement"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MetaWRAP</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=kegg_pathways_completeness" title="Compute KEGG pathway/module completeness from KOs or per-contig annotation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Calculate KEGG Pathways completeness</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bmtagger" title="remove contaminant reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bmtagger</button></a>
 <h3 id="qiime">Qiime</h3>
 <a href="https://usegalaxy.eu/root?tool_id=qiime_collapse_samples" title="Collapse samples in a BIOM table and mapping file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Collapse samples</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=qiime_make_otu_table" title="Make an OTU table from an OTU map and a taxonomy assignment file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Make OTU table</button></a>
@@ -2349,23 +2411,8 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=obi_annotate" title="Adds/Edits sequence record annotations"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">obiannotate</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=obi_ngsfilter" title="Assigns sequence records to the corresponding experiment/sample based on DNA tags and primers"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NGSfilter</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=obi_illumina_pairend" title="Construct consensus reads from Illumina pair-end reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Illuminapairedend</button></a>
-<h3 id="dataandmetadatamanagement">Data and Metadata Management</h3>
-<a href="https://usegalaxy.eu/root?tool_id=makeeml" title="Create EML from EAL templates"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Make EML</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=eml2eal" title="Create EAL templates from EML metadata"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">EML to EAL</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=eal_templates" title="for core features of a data package for EML metadata creation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Make templates</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=eal_table_template" title="attributes and categorical variables for EML metadata creation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Make templates for data tables</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=geo_cov_template" title="for EML metadata creation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Make geographic coverage template</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=taxo_cov_template" title="for EML metadata creation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Make taxonomic coverage template</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=raster_template" title="attributes for EML metadata creation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Make templates for raster files</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=vector_template" title="attributes for EML metadata creation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Make templates for vector files</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=entities_template" title="for EML metadata creation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Make entities templates for raster, vector and other entities files</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=annotations_template" title="from scratch or from EML metadata file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Make annotations template</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=eml_validate" title="check if your EML file is valid"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Eml validate:</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=data_paper_from_EML" title="from EML"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Make data paper sketches</button></a>
 <h3 id="virology">Virology</h3>
-<a href="https://usegalaxy.eu/root?tool_id=freyja_demix" title="lineage abundances"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Freyja: Demix</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=varvamp" title="design primers for highly diverse viruses"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">varVAMP</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=irma" title="Construct robust assemblies of highly variable RNA viruses"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">IRMA</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=snipit" title="Summarise snps relative to a reference sequence"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">snipit</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ivar_consensus" title="Call consensus from aligned BAM file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ivar consensus</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ivar_removereads" title="Remove reads from trimmed BAM file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ivar removereads</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ivar_trim" title="Trim reads in aligned BAM"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ivar trim</button></a>
@@ -2374,20 +2421,21 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=ivar_filtervariants" title="Filter variants across replicates or multiple samples aligned using the same reference"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ivar filtervariants</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=snpfreqplot" title="Generates a heatmap of allele frequencies grouped by variant type for SnpEff-annotated SARS-CoV-2 data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Variant Frequency Plot</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=read_it_and_keep" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Read It and Keep</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=snipit" title="Summarise snps relative to a reference sequence"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">snipit</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=freyja_variants" title="and get sequencing depth information"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Freyja: Call variants</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=freyja_demix" title="lineage abundances"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Freyja: Demix</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=freyja_boot" title="method"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Freyja: Bootstrapping</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=freyja_aggregate_plot" title="demixed results"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Freyja: Aggregate and visualize</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=cooc_mutbamscan" title="scans an alignment file for mutation co-occurrences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Cojac: mutbamscan</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=cooc_pubmut" title="pretty-prints cojac mutbamscan co-occurrence results"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Cojac: pubmut</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=cooc_tabmut" title="exports co-occurrence results from mutbamscan as a table"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Cojac: tabmut</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=lineagespot" title="identifies SARS-CoV-2 lineages contributing to metagenomic samples from per-sample variant files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">lineagespot</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=varvamp" title="design primers for highly diverse viruses"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">varVAMP</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=virheat" title="from VCFs as a heatmap and map mutations to respective genes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VirHEAT: visualize allele frequencies</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=irma" title="Construct robust assemblies of highly variable RNA viruses"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">IRMA</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=vapor" title="Classify Influenza samples from short reads sequence data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VAPOR</button></a>
 <hr/><h2 id="proteomics,metabolomics,chemistry">Proteomics, Metabolomics, Chemistry</h2>
 <h3 id="proteomics">Proteomics</h3>
-<a href="https://usegalaxy.eu/root?tool_id=proteinortho" title="detects orthologous proteins/genes within different species"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Proteinortho</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=proteinortho_grab_proteins" title="finds genes/proteins in a given fasta file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Proteinortho grab proteins</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=fragpipe" title="Data analysis for mass spectrometry-based proteomics"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FragPipe -  Academic Research and Education User License (Non-Commercial)</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=swissmodel_modelling_api" title="Fully automated protein structure homology-modelling"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SWISS-MODEL Modelling API</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=maxquant" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MaxQuant</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=msstatstmt" title="protein significance analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MSstatsTMT</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=msstats" title="statistical relative protein significance analysis in DDA, SRM and DIA Mass Spectrometry"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MSstats</button></a>
@@ -2603,6 +2651,8 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=pyprophet_protein" title="Protein error-rate estimation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PyProphet protein</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=pyprophet_subsample" title="Subsample OpenSWATH file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PyProphet subsample</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=proteinortho_summary" title="summaries the orthology-pairs/RBH files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Proteinortho summary</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=proteinortho_grab_proteins" title="finds genes/proteins in a given fasta file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Proteinortho grab proteins</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=proteinortho" title="detects orthologous proteins/genes within different species"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Proteinortho</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=flashlfq" title="ultrafast label-free quantification for mass-spectrometry proteomics"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FlashLFQ</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=quantwiz_iq" title="Isobaric Quantitation using QuantWiz-IQ"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">QuantWiz-IQ</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=peptide_genomic_coordinate" title="Get Peptide's genomic coordinate using mzsqlite DB and genomic mapping sqlite DB"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Peptide Genomic Coordinate</button></a>
@@ -2624,9 +2674,13 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=msgfplus" title="Identifies peptides in tandem mass spectra using the MS-GF+ search engine."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MS-GF+</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=eden_protease_prediction" title="based on cleavage sites"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Protease prediction</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=bg_protein_properties" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Calculate protein properties</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bioconductor_scp" title="single cell proteomics data analysis workflow"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bioconductor-scp</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=diann" title="is a software for DIA/SWATH data processing"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">DIA-NN</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=RTPredict" title="Predicts retention times for peptides using a model trained by RTModel."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RTPredict</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=iedb_netmhciipan" title="MHCii Binding prediction"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NetMHCiiPan</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=iedb_netmhcpan" title="MHC Binding prediction"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NetMHCPan</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=fragpipe" title="Data analysis for mass spectrometry-based proteomics"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FragPipe -  Academic Research and Education User License (Non-Commercial)</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=fragpipe_manifest_generator" title="Generate a FragPipe Manifest File (Experimental Design File)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FragPipe Manifest Generator</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=eggnog_mapper_annotate" title="annotation phase"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">eggNOG Mapper</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=eggnog_mapper_search" title="search phase"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">eggNOG Mapper</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=PTPredict" title="predicts the likelihood of peptides to be proteotypic via svm_model which is trained by PTModel"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PTPredict</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=InspectAdapter" title="Annotates MS/MS spectra using Inspect."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">InspectAdapter</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=InclusionExclusionListCreator" title="Creates inclusion and/or exclusion lists."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">InclusionExclusionListCreator</button></a>
@@ -2668,20 +2722,16 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=pepquery2_show_sets" title="PepQueryDB datasets, Parameters, PTMs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PepQuery2 Show Sets</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=pepquery2_index" title="MS/MS data for faster search"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PepQuery2 index</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=calisp" title="Estimate isotopic composition of peptides from proteomics mass spectrometry data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">calisp</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=eggnog_mapper_annotate" title="annotation phase"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">eggNOG Mapper</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=eggnog_mapper_search" title="search phase"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">eggNOG Mapper</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=diann" title="is a software for DIA/SWATH data processing"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">DIA-NN</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=SageAdapter" title="Annotates MS/MS spectra using Sage"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SageAdapter</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=OpenMSInfo" title="Prints configurations details of OpenMS"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">OpenMSInfo</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=JSONExporter" title="Exports .oms (SQLite) files in JSON format"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">JSONExporter</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ZeissLMDconverter" title="Converts tabular coordinates into a formatted text file readable by Zeiss laser-capture microdissection systems."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Zeiss laser-capture microdissection converter</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bioconductor_scp" title="single cell proteomics data analysis workflow"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bioconductor-scp</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=constava" title="calculates conformational-state probabilities and variability in structural ensembles"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Constava</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cardinal_group_comparison" title="performs two group comparisons of  mass spectrometry imaging data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MSI group comparison</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=pvacbind" title="The pVACbind tool of the pVACtools suite."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">pVACbind</button></a>
 <h3 id="metabolomics">Metabolomics</h3>
-<a href="https://usegalaxy.eu/root?tool_id=isolib" title="create an isotopic pattern library for given compounds and adducts based on enviPat"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">isolib</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=waveica" title="removal of batch effects for untargeted metabolomics data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">WaveICA</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=matchms_filtering" title="filter and normalize mass spectrometry data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">matchms filtering</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=matchms_add_key" title="Set metadata key in MSP to static value"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">matchms add key</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=msmetaenhancer" title="annotate MS data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MSMetaEnhancer</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=gem_flux_distribution" title="of a GEM"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Calculate flux distribution</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=table_scipy_interpolate" title="interpolate data using the scipy.interpolate library"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">table scipy interpolate</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=dimspy_align_samples" title="- Align peaks across Peaklists"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Align Samples</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=dimspy_replicate_filter" title="- Remove peaks that fail to appear in at least x-out-of-n (technical) replicates"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Replicate Filter</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=dimspy_process_scans" title="- Read, filter and average MS scans"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Process Scans (and SIM-Stitch)</button></a>
@@ -2766,12 +2816,14 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=recetox_aplcms_compute_template" title="compute retention time correction template feature table"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">recetox-aplcms - compute template</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=recetox_aplcms_align_features" title="align peaks across samples"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">recetox-aplcms - align features</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=rmassbank" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RMassBank</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=biotransformer" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BioTransformer</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=biotransformer" title="Generate biotransformation products for molecules."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BioTransformer</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=msmetaenhancer" title="collect and convert chemical identifiers in tables or MS libraries"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MSMetaEnhancer</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=riassigner" title="compute retention indices"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RIAssigner</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ramclustr" title="A feature clustering algorithm for non-targeted mass spectrometric metabolomics data."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RAMClustR</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ramclustr_define_experiment" title="Definition of experimental design used for record keeping and writing spectra data."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RAMClustR define experiment</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=recetox_xmsannotator_advanced" title="annotate peak intensity table including scores and confidence levels"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">recetox-xMSannotator</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=matchms_convert" title="convert between mass spectral library formats (.mgf/.msp/.json) using matchms"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">matchms convert</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=matchms_filtering" title="filter and normalize mass spectrometry data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">matchms filtering</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=matchms_fingerprint_similarity" title="calculate similarity between molecular fingerprints calculated from structural spectrum metadata descriptors"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">matchms fingerprint similarity</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=matchms_formatter" title="reformat scores object of matchms to long format table"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">matchms scores formatter</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=matchms_metadata_export" title="extract all metadata from mass spectra file to tabular format"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">matchms metadata export</button></a>
@@ -2780,6 +2832,7 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=matchms_similarity" title="calculate the similarity score and matched peaks"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">matchms similarity</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=matchms_spectral_similarity" title="matchms spectral similarity calculation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">matchms spectral similarity</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=matchms_split" title="split a large library into subsets"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">matchms split library</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=waveica" title="removal of batch effects for untargeted metabolomics data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">WaveICA</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=dimet_abundance_plot" title="Figures of metabolites total abundance as barplots (by DIMet)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">dimet abundance plot</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=dimet_differential_analysis" title="Differential analysis of tracer metabolomics data comparing two groups (by DIMet)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">dimet differential analysis</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=dimet_differential_multigroup_analysis" title="Differential analysis of 3 or more chosen groups of tracer metabolomics data (by DIMet)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">dimet differential multigroup analysis</button></a>
@@ -2792,6 +2845,7 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=mzmine_batch" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MZMine batch</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=matchms_subsetting" title="Extract spectra from a library given unique metadata identifier"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">matchms subsetting</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=matchms_metadata_merge" title="Merge metadata csv into MSP by a specified column"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">matchms metadata merge</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=matchms_add_key" title="Set metadata key in MSP to static value"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">matchms add key</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=matchms_remove_key" title="Remove metadata entry for all spectra in a library"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">matchms remove key</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=recetox_msfinder" title="Annotation of fragment peaks in mass spectral libraries."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RECETOX MsFinder</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=dimet_bivariate_analysis" title="Computation of the correlation of MDV profiles, or the metabolite time course profiles (by DIMet)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">dimet bivariate analysis</button></a>
@@ -2799,21 +2853,10 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=riassigner_from_comment" title="Assign different retention indices from unstructured comment metadata"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RIAssigner init from comment</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=tracegroomer" title="TraceGroomer is a solution to format and normalize files for DIMet tool"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">tracegroomer</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=sirius_csifingerid" title="is used to identify metabolites using single and        tandem mass spectrometry"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SIRIUS-CSI:FingerID</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=isolib" title="create an isotopic pattern library for given compounds and adducts based on enviPat"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">isolib</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=gc_derivatization" title="In silico MeOX and TMS derivatization tool"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GC derivatization</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=matchms_remove_spectra" title="Filters spectra based on metadata presence"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">matchms remove spectra</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=skyline2isocor" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Skyline2Isocor: converting skyling outputs into IsoCor inputs</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bioconductor_msnbase_smooth_mz" title="smooth raw MS data in mass-to-charge ratio domain"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bioconductor-msnbase smooth mz</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bioconductor_msnbase_smooth_chromatogram" title="smooth consecutive spectra using a moving window filter (combineSpectraMovingWindow)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bioconductor-msnbase smooth chromatogram</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bioconductor_msnbase_centroid" title="centroid raw profile-mode MS data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bioconductor-msnbase centroid</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=table_pandas_arithmetics" title="perform arithmetic operations on a dataframe column"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">table arithmetics</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=table_pandas_transform" title="apply transformations on multiple columns"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">table column transformations</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=table_pandas_rename_column" title="of a table"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">table rename column</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=gem_extract_exchange" title="of a GEM"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Get exchange bounds</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=table_pandas_rename_columns_regex" title="rename columns in a table using regex"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">table rename columns via regex</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=gem_escher_visualization" title="of a GEM using Escher"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Pathway visualization</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=gem_check_memote" title="using memote"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Make GEM quality report</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=target_screen" title="Extract peaks from recetox-aplcms tables using a list of target ions"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MS Target Screening</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=rcx-tk" title="Processes and standardizes metadata or alkane files by rearranging columns, validating file names, and deriving new columns for downstream analysis."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">rcx-tk</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=rename_annotated_feature" title="Rename columns in abundance table based on annotations table"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Rename Annotated Feature</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=spec2vec_similarity" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">spec2vec similarity</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=spec2vec_training" title="Train a Spec2Vec model for mass spectra similarity scoring"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">spec2vec model training</button></a>
@@ -2825,80 +2868,49 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=mfassignr_mfassignCHO" title="Molecular formula assignment (only with CHO)."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MFAssignR MFAssignCHO</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=mfassignr_recal" title="Internal mass recalibration using a recalibrant series."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MFAssignR Recal</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=mfassignr_recallist" title="Identification of candidate series for recalibration."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MFAssignR RecalList</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=rcx-tk" title="Processes and standardizes metadata or alkane files by rearranging columns, validating file names, and deriving new columns for downstream analysis."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">rcx-tk</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=mfassignr_findRecalSeries" title="Selects most suitable series for recalibration"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MFAssignR FindRecalSeries</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ms2deepscore_config_generator" title="Generates model parameters for MS2DeepScore in JSON format"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MS2DeepScore Configuration Generator</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ms2deepscore_similarity" title="Compute similarity scores using a pre-trained MS2DeepScore model"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MS2DeepScore Similarity</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ms2deepscore_training" title="Compute similarity scores using a pre-trained MS2DeepScore model"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MS2DeepScore Model Training</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=target_screen" title="Extract peaks from recetox-aplcms tables using a list of target ions"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MS Target Screening</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=mixmodel4repeated_measures" title="ANOVA for repeated measures statistics"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">mixmodel</button></a>
-<h3 id="chemicaltoolbox">ChemicalToolBox</h3>
-<a href="https://usegalaxy.eu/root?tool_id=ctb_mds_plot" title="of molecule similarity"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MDS Scatter Plot</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ctb_confab" title="for molecules (confab)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Conformer calculation</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ctb_online_data_fetch" title="fetching ..."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Online data</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ambertools_acpype" title="using acpype"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Generate MD topologies for small molecules</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ctb_pubchem_download_assays" title="as canonical SMILES"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PubChem Assay Downloader</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=chembl" title="for compounds which are similar to a SMILES string"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Search ChEMBL database</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ambertools_antechamber" title="- Amber's molecular input file processor"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">AnteChamber</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bioconductor_msnbase_smooth_mz" title="smooth raw MS data in mass-to-charge ratio domain"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bioconductor-msnbase smooth mz</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bioconductor_msnbase_smooth_chromatogram" title="smooth consecutive spectra using a moving window filter (combineSpectraMovingWindow)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bioconductor-msnbase smooth chromatogram</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bioconductor_msnbase_centroid" title="centroid raw profile-mode MS data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bioconductor-msnbase centroid</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=table_pandas_arithmetics" title="perform arithmetic operations on a dataframe column"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">table arithmetics</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=table_scipy_interpolate" title="interpolate data using the scipy.interpolate library"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">table scipy interpolate</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=table_pandas_transform" title="apply transformations on multiple columns"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">table column transformations</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=table_pandas_rename_column" title="of a table"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">table rename column</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=table_pandas_rename_columns_regex" title="rename columns in a table using regex"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">table rename columns via regex</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=gem_extract_exchange" title="of a GEM"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Get exchange bounds</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=gem_flux_distribution" title="of a GEM"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Calculate flux distribution</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=gem_escher_visualization" title="of a GEM using Escher"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Pathway visualization</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=gem_check_memote" title="using memote"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Make GEM quality report</button></a>
+<h3 id="chemicaltoolbox">ChemicalToolBox</h3>
+<a href="https://usegalaxy.eu/root?tool_id=ambertools_acpype" title="using acpype"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Generate MD topologies for small molecules</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=chembl" title="for compounds which are similar to a SMILES string"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Search ChEMBL database</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ambertools_antechamber" title="- Amber's molecular input file processor"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">AnteChamber</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=parmconv" title="to AMBER prmtop in preparation for MMGBSA/MMPBSA"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert Parameters</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ctb_openmg" title="Exhaustive generation of chemical structures"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Open Molecule Generator</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ambertools_parmchk2" title="- Amber's parameter checker"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ParmChk2</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=prepare_receptor" title="Tool to prepare receptor for docking with Autodock Vina"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Prepare receptor</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=traj_selections_and_merge" title="- select specific molecules and merge multiple trajectories."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Trajectory select and merge</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=md_converter" title="- interconvert between MD trajectory file formats."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MDTraj file converter</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=mmpbsa_mmgbsa" title="tool for estimating ligand binding affinities"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MMPBSA/MMGBSA</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=sucos_docking_scoring" title="- compare shape and feature overlap of docked ligand poses to a reference molecule"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Score docked poses using SuCOS</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=gmx_solvate" title="to structure and topology files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GROMACS solvation and adding ions</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=gmx_md" title="for data collection"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GROMACS production simulation</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=biomd_neqgamma" title="for calculating friction and free energy profiles from TMD ensembles"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">dcTMD friction correction</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=md_slicer" title="using the MDTraj package"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Slice MD trajectories</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=prepare_box" title="for an AutoDock Vina job from a ligand or pocket input file (confounding box)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Calculate the box parameters using RDKit</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ctb_silicos_qed" title="quantitative estimation (QED) with RDKit"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Drug-likeness</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=gmx_sim" title="for system equilibration or data collection"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GROMACS simulation</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ctb_alignit" title="and optimization (Align-it)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Pharmacophore alignment</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ctb_alignit_create_db" title="generation (Align-it)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Pharmacophore</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=gmx_editconf" title="using editconf"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GROMACS structure configuration</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=dpocket" title="to calculate descriptors for protein pockets"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">dpocket</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=fpocket" title="- find potential binding sites in protein structures"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">fpocket</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=gmx_makendx" title="using make_ndx"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Create GROMACS index files</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=gmx_setup" title="of topology and GRO structure file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GROMACS initial setup</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=gmx_em" title="of the system prior to equilibration and production MD"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GROMACS energy minimization</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=gmx_merge_topology_files" title="and GRO files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Merge GROMACS topologies</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=gmx_trj" title="using trjconv and trjcat"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Modify/convert and concatate GROMACS trajectories</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=gmx_energy" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Extract energy components with GROMACS</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=gmx_restraints" title="using genrestr"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Create GROMACS position restraints files</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=gmx_rg" title="of a molecular structure"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GROMACS Radius of Gyration</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=acpype_Amber2Gromacs" title="using acpype"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert Amber topology and coordinate files to GROMACS format</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=docking" title="tool to perform protein-ligand docking with Autodock Vina"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VINA Docking</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=tleap" title="interactively build and run tLEaP files to set up systems with AmberTools"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Build tLEaP</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=alphafold" title="- AI-guided 3D structural prediction of proteins"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Alphafold 2</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=gromacs_modify_topology" title="to a GROMACS topology file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Adding New Topology Information</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=gromacs_extract_topology" title="from a GROMACS topology file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Extracting Topology Information</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=gmx_get_builtin_file" title="from built-in datasets"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GROMACS copy file</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=pdbfixer" title="to automatically fix a PDB file before performing molecular dynamics simulation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PDBFixer</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=gmx_check" title="to provide information about GROMACS input files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GROMACS check</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=gmx_rmsd" title="of molecular structures"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GROMACS RMSD calculation</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=gmx_rmsf" title="of molecular structures"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GROMACS RMSF calculation</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=xtb_molecular_optimization" title="Semiempirical quantum mechanical molecular optimization method"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">xtb molecular optimization</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=rem_complex" title="Remove molecular coordination complexes from a list of structure representations"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Remove coordination complexes</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=qcxms_neutral_run" title="required as first step to prepare for the production runs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">QCxMS neutral run</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=qcxms_production_run" title="Production run to obtain a QCxMS simulated mass spectrum"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">QCxMS production run</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=qcxms_getres" title="Get result of the Production run to obtain a QCxMS simulated mass spectrum"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">QCxMS get results</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=qiskit_xyz2pdb" title="alpha carbon PDB files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert Qiskit's XYZ files to</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=pulchra" title="from reduced representations"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PULCHRA recontruction of all atom proteins</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=biopdb_align_and_rmsd" title="using Biopython"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Align structures and compute relative RMSDs</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=openbabel_obgrep" title="- an advanced molecular search program using SMARTS"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Compound search</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=openbabel_genProp" title="for a set of molecules"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Compute physico-chemical properties</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=openbabel_svg_depiction" title="of compounds"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Visualisation</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=openbabel_spectrophore_search" title="- similarity search based on 1D chemical features"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Spectrophores search</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=openbabel_compound_convert" title="- interconvert between various chemistry and molecular modeling data files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Compound conversion</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=gmx_energy" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Extract energy components with GROMACS</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=gmx_trj" title="using trjconv and trjcat"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Modify/convert and concatate GROMACS trajectories</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=gmx_sim" title="for system equilibration or data collection"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GROMACS simulation</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=gmx_em" title="of the system prior to equilibration and production MD"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GROMACS energy minimization</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=gmx_setup" title="of topology and GRO structure file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GROMACS initial setup</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=openbabel_subsearch" title="of fingerprint data sets"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Substructure Search</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=lirasearch" title="using LiraSearch spherical harmonic descriptors"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Identify similar conformers</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=diffdock" title="Predict ligand binding poses using DiffDock's diffusion-based docking method"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">diffdock</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=biomd_rmsd_clustering" title="from MD RMSD matrix data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Hierarchical clustering</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=biomd_extract_clusters" title="from linkage matrix data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Extract clusters of MD trajectories</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=mdanalysis_extract_rmsd" title="from MD ensemble with MDAnalysis"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Extract RMSD distance matrix data</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=openbabel_addh" title="at a certain pH value"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Add hydrogen atoms</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=openbabel_remIons" title="from a library of compounds"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Remove counterions and fragments</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=chembl_structure_pipeline" title="for curation and standardizing of molecular structures"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ChEMBL structure pipeline</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=biomd_neqgamma" title="for calculating friction and free energy profiles from TMD ensembles"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">dcTMD friction correction</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=openbabel_remove_protonation_state" title="of every atom"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Remove protonation state</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=mdanalysis_ramachandran_protein" title="- Ramachandran plot for proteins"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Ramachandran Analysis</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=mdanalysis_endtoend" title="- End-to-End distance timeseries and histogram for the given selections"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">End-to-End Analysis</button></a>
@@ -2910,20 +2922,31 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=OpenPepXL" title="Tool for protein-protein cross-linking identification using labeled linkers."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">OpenPepXL</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=openbabel_change_title" title="to metadata value."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Change title</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=mdanalysis_rdf" title="- Radial Distribution Function between two atoms"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RDF Analysis</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=openbabel_spectrophore_search" title="- similarity search based on 1D chemical features"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Spectrophores search</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=mdanalysis_angle" title="- time series of Angles"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Angle Analysis</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=apoc" title="Large-scale structural comparison of protein pockets"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">APoc</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=smina" title="Scoring and Minimization"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">smina</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=prepare_receptor" title="Tool to prepare receptor for docking with Autodock Vina"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Prepare receptor</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=enumerate_charges" title="calculated with Dimorphite DL and RDKit"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Enumerate changes</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=sdf_to_tab" title="into a tabular file using RDKit"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Extract values from an SD-file</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=fpocket" title="- find potential binding sites in protein structures"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">fpocket</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ctb_mordred_descriptors" title="with Mordred"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Calculate molecular descriptors</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ctb_pubchem_download_as_smiles" title="as canonical SMILES"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PubChem Download</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ctb_pubchem_download_assays" title="as table"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PubChem Assay Downloader</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=docking" title="tool to perform protein-ligand docking with Autodock Vina"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VINA Docking</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=prepare_ligand" title="for docking with Autodock Vina"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Prepare ligand</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=prepare_box" title="for an AutoDock Vina job from a ligand or pocket input file (confounding box)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Calculate the box parameters using RDKit</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=openbabel_remDuplicates" title="from a library of compounds"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Remove duplicated molecules</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=openbabel_filter" title="a set of molecules from a file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Filter</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=openbabel_compound_convert" title="- interconvert between various chemistry and molecular modeling data files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Compound conversion</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=openbabel_svg_depiction" title="of compounds"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Visualisation</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=openbabel_genProp" title="for a set of molecules"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Compute physico-chemical properties</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=openbabel_obgrep" title="- an advanced molecular search program using SMARTS"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Compound search</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=openbabel_remSmall" title="from a library of compounds"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Remove small molecules</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=prepare_ligands_for_docking" title="Tool to prepare ligands for docking with tools like Autodock Vina"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Prepare ligands for docking</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ctb_rdkit_descriptors" title="calculated with RDKit"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Descriptors</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ctb_silicos_qed" title="quantitative estimation (QED) with RDKit"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Drug-likeness</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=sucos_docking_scoring" title="- compare shape and feature overlap of docked ligand poses to a reference molecule"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Score docked poses using SuCOS</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=sucos_clustering" title="based on the overlap of 3D features"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Cluster ligands using SuCOS</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=sucos_max_score" title="- determine maximum SuCOS score of ligands against clustered fragment hits"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Max SuCOS score</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=openbabel_structure_distance_finder" title="- determine the minimum distances between a molecule and a set of 3D points"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Determine distance to defined points</button></a>
@@ -2947,6 +2970,7 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=ctb_im_screen" title="a compound against a library using RDKit"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Screen</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ctb_im_xcos" title="scoring"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">XCos</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=featurestein" title="feature overlay scoring"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">'FeatureStein' fragment overlay scoring</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=gmx_merge_topology_files" title="and GRO files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Merge GROMACS topologies</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=openduck_chunk" title="for dynamic undocking"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">OpenDUck chunk</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=openduck_run_smd" title="steered molecular dynamics runs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Run OpenDUck</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=xchem_transfs_scoring" title="using deep learning"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">XChem TransFS pose scoring</button></a>
@@ -2954,8 +2978,10 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=ctb_chemfp_nxn_clustering" title="of molecular fingerprints"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NxN clustering</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ctb_chemfp_butina_clustering" title="of molecular fingerprints"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Taylor-Butina clustering</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ctb_sdf2fps" title="- extract fingerprints from sdf file metadata"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SDF to Fingerprint</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=md_converter" title="- interconvert between MD trajectory file formats."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MDTraj file converter</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=fastpca" title="- dimensionality reduction of MD simulations"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">fastpca</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=rdconf" title="using RDKit"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RDConf: Low-energy ligand conformer search</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=traj_selections_and_merge" title="- select specific molecules and merge multiple trajectories."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Trajectory select and merge</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=alchemical_analysis" title="Analysis of alchemical free energy calculations"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Alchemical Analysis</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=vmd_hbonds" title="between two segments of a trajectory"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Hydrogen Bond Analysis using VMD</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=bio3d_pca_visualize" title="- generate trajectories of principal components of atomic motion"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PCA visualization</button></a>
@@ -2963,6 +2989,7 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=bio3d_pca" title="- principal component analysis using Bio3D"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PCA</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=bio3d_rmsd" title="using Bio3D"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RMSD Analysis</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=bio3d_dccm" title="- Dynamical Cross-Correlation Maps using Bio3D (DCCM)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">DCCM analysis</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=md_slicer" title="using the MDTraj package"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Slice MD trajectories</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=packmol" title="- initial configurations for molecular dynamics simulations by packing optimization"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PACKMOL</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=padel" title="calculator"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PaDEL descriptor</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ctb_online_data_fetch" title="fetching"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Online data</button></a>
@@ -2975,9 +3002,39 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=ctb_osra" title="in PDF documents (OSRA)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Molecule recognition</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ctb_np-likeness-calculator" title="likeness calculator"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Natural Product</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ctb_simsearch" title="of fingerprint data sets"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Similarity Search</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ctb_confab" title="for molecules (confab)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Conformer calculation</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ctb_mds_plot" title="of molecule similarity"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MDS Scatter Plot</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ctb_online_data_fetch" title="fetching ..."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Online data</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=fragmenter" title="splits a molecule in fragments"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Fragmenter</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ctb_pubchem_download_assays" title="as canonical SMILES"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PubChem Assay Downloader</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=bgchem_fragment_merger" title="fragmented molecules"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Merging</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ctb_openmg" title="Exhaustive generation of chemical structures"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Open Molecule Generator</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=chembl_structure_pipeline" title="for curation and standardizing of molecular structures"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ChEMBL structure pipeline</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=gmx_md" title="for data collection"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GROMACS production simulation</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ctb_alignit" title="and optimization (Align-it)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Pharmacophore alignment</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ctb_alignit_create_db" title="generation (Align-it)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Pharmacophore</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=dpocket" title="to calculate descriptors for protein pockets"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">dpocket</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=gmx_rg" title="of a molecular structure"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GROMACS Radius of Gyration</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=acpype_Amber2Gromacs" title="using acpype"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert Amber topology and coordinate files to GROMACS format</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=tleap" title="interactively build and run tLEaP files to set up systems with AmberTools"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Build tLEaP</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=alphafold" title="- AI-guided 3D structural prediction of proteins"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Alphafold 2</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=gromacs_modify_topology" title="to a GROMACS topology file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Adding New Topology Information</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=gromacs_extract_topology" title="from a GROMACS topology file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Extracting Topology Information</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=gmx_get_builtin_file" title="from built-in datasets"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GROMACS copy file</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=pdbfixer" title="to automatically fix a PDB file before performing molecular dynamics simulation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PDBFixer</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=gmx_check" title="to provide information about GROMACS input files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GROMACS check</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=gmx_rmsd" title="of molecular structures"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GROMACS RMSD calculation</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=gmx_rmsf" title="of molecular structures"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GROMACS RMSF calculation</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=xtb_molecular_optimization" title="Semiempirical quantum mechanical molecular optimization method"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">xtb molecular optimization</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=rem_complex" title="Remove molecular coordination complexes from a list of structure representations"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Remove coordination complexes</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qcxms_neutral_run" title="required as first step to prepare for the production runs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">QCxMS neutral run</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qcxms_production_run" title="Production run to obtain a QCxMS simulated mass spectrum"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">QCxMS production run</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qcxms_getres" title="Get result of the Production run to obtain a QCxMS simulated mass spectrum"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">QCxMS get results</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiskit_xyz2pdb" title="alpha carbon PDB files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert Qiskit's XYZ files to</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=pulchra" title="from reduced representations"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PULCHRA recontruction of all atom proteins</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=biopdb_align_and_rmsd" title="using Biopython"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Align structures and compute relative RMSDs</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=lirasearch" title="using LiraSearch spherical harmonic descriptors"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Identify similar conformers</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=diffdock" title="Predict ligand binding poses using DiffDock's diffusion-based docking method"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">diffdock</button></a>
 <hr/><h2 id="statisticsandvisualisation">Statistics and Visualisation</h2>
 <h3 id="statistics">Statistics</h3>
 <a href="https://usegalaxy.eu/root?tool_id=maximal_information_based_nonparametric_exploration" title="- Maximal Information-based Nonparametric Exploration"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MINE</button></a>
@@ -2993,7 +3050,6 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=cca1" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Canonical Correlation Analysis</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=t_test_two_samples" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">T Test for Two Samples</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=scipy_sparse" title="for manipulating 2-D Scipy sparse numeric data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Sparse Matrix Functions</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=saqc" title="quality control for time series"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SaQC</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=create_tool_recommendation_model" title="using deep learning"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Create a model to recommend tools</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=dwt_var1" title="using Discrete Wavelet Transfoms"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Wavelet variance</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=graphembed" title="Compute and plot a 2D embedding of a data matrix given supervised class information"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GraphEmbed</button></a>
@@ -3008,16 +3064,11 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=rgcca" title="performs multiblock data analysis of several sets of variables (blocks) observed on the same group of individuals."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RGCCA</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=bg_statistical_hypothesis_testing" title="computes several descriptive statistics"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Statistical hypothesis testing</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=clustering_from_distmat" title="using Scipy"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Distance matrix-based hierarchical clustering</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=saqc" title="quality control pipelines for environmental sensor data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SaQC</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=fastspar" title="correlation estimation for compositional data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FastSpar</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=Summary_Statistics1" title="for any numerical column"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Summary Statistics</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=Count1" title="occurrences of each record"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Count</button></a>
 <h3 id="machinelearning">Machine Learning</h3>
-<a href="https://usegalaxy.eu/root?tool_id=flexynesis_utils" title="Utility functions for Flexynesis"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Flexynesis utils</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=json2yolosegment" title="with ultralytics"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert AnyLabeling JSON to YOLO text</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=flexynesis_cbioportal_import" title="and prepare cBioPortal data for Flexynesis analysis"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Flexynesis cBioPortal import</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=flexynesis_plot" title="tool for visualizing flexynesis results"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Flexynesis plot</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=tesseract" title="Optical Character Recognition"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Tesseract</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=flexynesis" title="A deep-learning based multi-omics bulk sequencing data integration suite"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Flexynesis</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=tabpfn" title="with PyTorch"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Tabular data prediction using TabPFN</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=sklearn_pca" title="with scikit-learn"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Principal component analysis</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=sklearn_lightgbm" title="- train and apply LightGBM models"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">LightGBM</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=sklearn_numeric_clustering" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Numeric Clustering</button></a>
@@ -3049,66 +3100,65 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=keras_model_config" title="using Keras"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Create a deep learning model architecture</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=scipy_sparse" title="for manipulating 2-D Scipy sparse numeric data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Sparse Matrix Functions</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=create_tool_recommendation_model" title="using deep learning"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Create a model to recommend tools</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=black_forest_labs_flux" title="text-to-image model"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FLUX</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=cleanlab_issue_handler" title="Detect and optionally clean data issues using Cleanlab"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Cleanlab Issue Handler</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=whisperx" title="Transcribe audio or video files to text using the OpenAI Whisper and speaker diarization (WhisperX)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Speech to Text with Diarization</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=chatgpt_openai_api" title="Integrating OpenAI's ChatGPT into Galaxy"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">chatGPT</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=sklearn_to_categorical" title="Converts a class vector (integers) to binary class matrix"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">To categorical</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=mcl" title="Markov Cluster Algorithm for graphs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MCL</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=virhunter" title="Deep learning method to identify viruses in sequencing datasets"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">virhunter</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=decontaminator" title="Decontaminator is a deep learning helping tool that filters out phage or fungi contigs from plant virome RNAseq assemblies"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">decontaminator</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=deepmicro" title="Representation learning and classification framework"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">DeepMicro</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=sklearn_label_encoder" title="Encode target labels with value between 0 and n_classes-1"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Label encoder</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=colorize_labels" title="with NetworkX"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Colorize label map</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=biomodels_biomd0000001076" title="proteins involved in cancer immunotherapy using molecular descriptors and Multi Layer Perceptron (MLP) neural network"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Prediction of Breast Cancer (BC)</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=biomodels_biomd0000001066" title="to predict efficacy of immune checkpoint blockade across multiple cancer patient cohorts"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Random Forest model</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=whisper" title="Transcribe audio or video files to text using the OpenAI Whisper"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Speech to Text</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=chatgpt_openai_api" title="Integrating OpenAI's ChatGPT into Galaxy"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">chatGPT</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=flexynesis" title="A deep-learning based multi-omics bulk sequencing data integration suite"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Flexynesis</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=black_forest_labs_flux" title="text-to-image model"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FLUX</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=tabpfn" title="with PyTorch"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Tabular data prediction using TabPFN</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=flexynesis_cbioportal_import" title="and prepare cBioPortal data for Flexynesis analysis"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Flexynesis cBioPortal import</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cleanlab_issue_handler" title="Detect and optionally clean data issues using Cleanlab"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Cleanlab Issue Handler</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=flexynesis_utils" title="Utility functions for Flexynesis"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Flexynesis utils</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=flexynesis_plot" title="tool for visualizing flexynesis results"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Flexynesis plot</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=whisperx" title="Transcribe audio or video files to text using the OpenAI Whisper and speaker diarization (WhisperX)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Speech to Text with Diarization</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=llm_hub" title="Call any LLM"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">LLM Hub</button></a>
+<h3 id="computervision">Computer vision</h3>
+<a href="https://usegalaxy.eu/root?tool_id=wildlife_megadetector_huggingface" title="Detect and classify wildlife species in images and videos using MegaDetector and Hugging Face models (AI)."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Wildlife Detection</button></a>
 <h3 id="graph/displaydata">Graph/Display Data</h3>
-<a href="https://usegalaxy.eu/root?tool_id=wordcloud" title="with highly customizable appearance"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Generate a word cloud</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=venn_list" title="from lists"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Venn Diagram</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=jbrowse_to_standalone" title="upgrades the bare data directory to a full JBrowse instance"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">JBrowse - Data Directory to Standalone</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=jbrowse" title="genome browser"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">JBrowse</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=pe_histogram" title="of insert size frequency"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Paired-end histogram</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=pretext_snapshot" title="image generator for Pretext contact maps"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Pretext Snapshot</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=volcanoplot" title="create a volcano plot"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Volcano Plot</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=intervene_pairwise" title="and heatmap for genomic intervals"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Pairwise intersection</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=intervene_upset" title="of intersection of genomic regions or list sets"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">UpSet diagram</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=build_ucsc_custom_track_1" title="for UCSC genome browser"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Build custom track</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=scatterplot_rpy" title="of two numeric columns"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Scatterplot</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=circos_aln_to_links" title="reformats alignment files to prepare for Circos"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Circos: Alignments to links</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=circos_binlinks" title="reduce links to a density plot"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Circos: Link Density Track</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=circos_bundlelinks" title="reduce numbers of links in datasets before plotting"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Circos: Bundle Links</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=circos" title="visualizes data in a circular layout"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Circos</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=circos_gc_skew" title="calculates skew over genomic sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GC Skew</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=histogram_rpy" title="of a numeric column"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Histogram</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=gmaj_1" title="Multiple Alignment Viewer"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GMAJ</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=XY_Plot_1" title="for multiple series and graph types"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Plotting tool</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=jvarkit_wgscoverageplotter" title="Plot read coverage across a genomic contig"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BAM Coverage Plotter</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=jbrowse_to_standalone" title="upgrades the bare data directory to a full JBrowse instance"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">JBrowse - Data Directory to Standalone</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=jbrowse" title="genome browser"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">JBrowse</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=pygenomeTracks" title="plot genomic data tracks"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">pyGenomeTracks</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=circos_interval_to_tile" title="reformats interval files to prepare for Circos tile plots"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Circos: Interval to Tiles</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=circos_resample" title="reduce numbers of points in a dataset before plotting"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Circos: Resample 1/2D data</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=circos_binlinks" title="reduce links to a density plot"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Circos: Link Density Track</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=circos_wiggle_to_scatter" title="reformats bigWig files to prepare for Circos 2d scatter/line/histogram plots"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Circos: bigWig to Scatter</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=circos_wiggle_to_stacked" title="reformats for use in Circos stacked histogram plots"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Circos: Stack bigWigs as Histogram</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=circos_tableviewer" title="easily creates circos plots from tabular data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Circos: Table viewer</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=circos_interval_to_text" title="reformats interval files to prepare for Circos text labels"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Circos: Interval to Circos Text Labels</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ggplot2_pca" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PCA plot w ggplot2</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=pygenomeTracks" title="plot genomic data tracks"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">pyGenomeTracks</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=pathview" title="for pathway based data integration and visualization"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Pathview</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ggplot2_heatmap2" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">heatmap2</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=histogram_rpy" title="of a numeric column"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Histogram</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=pathifier" title=": Quantify deregulation of pathways in cancer"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Pathifier</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bandage_image" title="visualize de novo assembly graphs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Bandage Image</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=gmaj_1" title="Multiple Alignment Viewer"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GMAJ</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=circos_aln_to_links" title="reformats alignment files to prepare for Circos"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Circos: Alignments to links</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=circos_tableviewer" title="easily creates circos plots from tabular data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Circos: Table viewer</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=circos_gc_skew" title="calculates skew over genomic sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GC Skew</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=circos_wiggle_to_stacked" title="reformats for use in Circos stacked histogram plots"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Circos: Stack bigWigs as Histogram</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=circos_bundlelinks" title="reduce numbers of links in datasets before plotting"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Circos: Bundle Links</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ggplot2_heatmap" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Heatmap w ggplot</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ggplot2_violin" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Violin plot w ggplot2</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ggplot2_point" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Scatterplot with ggplot2</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ggplot2_histogram" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Histogram with ggplot2</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bandage_info" title="determine statistics of de novo assembly graphs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Bandage Info</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=gene_iobio_display_generation_iframe" title="analyses VCFs for single and trio analysis to find causative variants using gene.iobio's public server"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">gene.iobio visualisation</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=edu.tamu.cpt.genome_viz.linear_genome_plot" title="Linear Genome Plot"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Linear Genome Plot</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=plotly_ml_performance_plots" title="of tabular data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Plot confusion matrix, precision, recall and ROC and AUC curves</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=jbrowse2" title="genome browser"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">JBrowse2</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=XY_Plot_1" title="for multiple series and graph types"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Plotting tool</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=jvarkit_wgscoverageplotter" title="Plot read coverage across a genomic contig"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BAM Coverage Plotter</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=newick_display" title="visualize a phylogenetic tree"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Newick Display</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bandage_info" title="determine statistics of de novo assembly graphs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Bandage Info</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bandage_image" title="visualize de novo assembly graphs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Bandage Image</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=intervene_upset" title="of intersection of genomic regions or list sets"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">UpSet diagram</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=intervene_pairwise" title="and heatmap for genomic intervals"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Pairwise intersection</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=pathview" title="for pathway based data integration and visualization"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Pathview</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=export2graphlan" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Export to GraPhlAn</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=venn_list" title="from lists"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Venn Diagram</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=volcanoplot" title="create a volcano plot"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Volcano Plot</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ggplot2_heatmap2" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">heatmap2</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=plotly_regression_performance_plots" title="of tabular data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Plot actual vs predicted curves and residual plots</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=plotly_parallel_coordinates_plot" title="of tabular data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Parallel Coordinates Plot</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ggplot2_pca" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PCA plot w ggplot2</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=four_color_plot" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Fasta nucleotide color plot</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=graphlan" title="to produce graphical output of an input tree"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GraPhlAn</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=graphlan_annotate" title="for GraPhlAn"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Generation, personalization and annotation of tree</button></a>
@@ -3117,8 +3167,16 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=fasta_nucleotide_color_plot" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Fasta nucleotide color plot</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=mummerplot_wrapper" title="Combine mummer/nucmer/promer with mummerplot"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MUMmer dotplot</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=karyotype_Plot_1" title="for multiple series"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Karyotype Plotting tool</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=pe_histogram" title="of insert size frequency"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Paired-end histogram</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=pretext_snapshot" title="image generator for Pretext contact maps"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Pretext Snapshot</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=circos" title="visualizes data in a circular layout"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Circos</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=barchart_gnuplot" title="for multiple columns"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Bar chart</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=pathifier" title=": Quantify deregulation of pathways in cancer"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Pathifier</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=qual_stats_boxplot" title="of quality statistics"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Boxplot</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=gene_iobio_display_generation_iframe" title="analyses VCFs for single and trio analysis to find causative variants using gene.iobio's public server"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">gene.iobio visualisation</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=edu.tamu.cpt.genome_viz.linear_genome_plot" title="Linear Genome Plot"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Linear Genome Plot</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=jbrowse2" title="genome browser"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">JBrowse2</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=wordcloud" title="with highly customizable appearance"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Generate a word cloud</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=vcf_to_maf_customtrack1" title="for display at UCSC"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VCF to MAF Custom Track</button></a>
 <h3 id="muonspectroscopy">Muon Spectroscopy</h3>
 <a href="https://usegalaxy.eu/root?tool_id=cif2cell" title="convert .cif file to .cell"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">cif2cell</button></a>
@@ -3131,11 +3189,147 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=pm_muairss_read" title="run clustering for optimised structures"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PyMuonSuite AIRSS Cluster</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=muspinsim_combine" title="combine datafiles generated from MuSpinSim"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MuSpinSim Combine</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=mudirac" title="Muonic atom Dirac equation solver"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MuDirac</button></a>
+<h3 id="xas(x-rayabsorptionspectroscopy)">XAS (X-ray Absorption Spectroscopy)</h3>
+<a href="https://usegalaxy.eu/root?tool_id=larch_select_paths" title="select FEFF paths for XAFS data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Larch Select Paths</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=larch_plot" title="plot Athena projects"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Larch Plot</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=larch_athena" title="generate Athena projects from XAFS data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Larch Athena</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=larch_artemis" title="generate Artemis projects from XAFS data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Larch Artemis</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=larch_feff" title="generate FEFF paths from XAFS data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Larch FEFF</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=larch_lcf" title="perform linear combination fit on XAS data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Larch LCF</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=larch_criteria_report" title="generate reports on Artemis fitting from XAFS data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Larch Criteria Report</button></a>
+<hr/><h2 id="ecology">Ecology</h2>
+<h3 id="ecoregionalization">Ecoregionalization</h3>
+<a href="https://usegalaxy.eu/root?tool_id=ecoregion_brt_analysis" title="for species distribution modelling"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BRT tool prediction</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ecoregion_taxa_seeker" title="for recover list of taxa"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">TaxaSeeker</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ecoregion_eco_map" title="Create map from cluster to visualize ecoregions"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">EcoMap</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ecoregion_cluster_estimate" title="Find an optimal number of cluster with SIH index"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ClusterEstimate</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ecoregion_clara_cluster" title="Make cluster from BRT prediction with Clara algorithm"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ClaraClust</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ecoregion_GeoNearestNeighbor" title="Merge two data tables by finding the closest points based on latitude and longitude coordinates (WGS84 projection)."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GeoNearestNeighbor</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ClaraGuess" title="Environmental clustering using CLARA and BRT predictions"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Clara Estimate and Clustering</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=indicspecies" title="to identify indicator species within clusters/groups"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Indicspecies</button></a>
+<h3 id="phylodiversity">Phylodiversity</h3>
+<a href="https://usegalaxy.eu/root?tool_id=crsconverter" title="from environmental predictors for species distribution modeling"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CRSconverter</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=phylogenetic_occupancy_matcher" title="match phylogenetic and occupancy data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PhylOccuMatcher</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=estimate_endem" title="of each cell of a spatial grid"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">EstimEndem</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=phylo_index" title="compute phylodiversity index based on matched phylogenetic and occupancy data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PhyloIndex</button></a>
+<h3 id="indicatorsfromgeometricmean">Indicators from geometric mean</h3>
+<a href="https://usegalaxy.eu/root?tool_id=Map_shp" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Make a map with a shapefile</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=Mean_geom" title="- calcul of the geometric means for the 'bois mort' indicator"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Geometric means</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bar_plot" title="for simple discrete data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Bar plot</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=divand_full_analysis" title="Data-Interpolating Variational Analysis in n dimensions"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">DIVAnd</button></a>
+<h3 id="animaldetectiononacousticrecordings">Animal Detection on Acoustic Recordings</h3>
+<a href="https://usegalaxy.eu/root?tool_id=spocc_occ" title="from GBIF, ALA, iNAT and others"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Get species occurrences data</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=vigiechiro_bilanenrichipf" title="from Animal Detection on Acoustic Recordings"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Advanced restitution: 'Point fixe' protocol</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=vigiechiro_bilanenrichirp" title="from Animal Detection on Acoustic Recordings"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Advanced restitution: 'Routier'or 'Pedestre' protocols</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=vigiechiro_idcorrect_2ndlayer" title="clean data from animal detection on acoustic recordings"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Tadarida data cleaner</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=vigiechiro_idvalid" title="Integrate identifications from animal detection on acoustic recordings"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Tadarida identifications validation</button></a>
+<h3 id="computeindicatorsforsatelliteremotesensing">Compute indicators for satellite remote sensing</h3>
+<a href="https://usegalaxy.eu/root?tool_id=srs_pca" title="from remote sensing data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Compute a PCA raster</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=srs_diversity_maps" title="from remote sensing data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Map diversity</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=srs_preprocess_s2" title="read, crop, resample and write it as a raster stack"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Preprocess sentinel 2 data</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=srs_spectral_indices" title="as NDVI from remote sensing data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Compute spectral indices</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=srs_process_data" title="with remote sensing data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Compare diversity indicators</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=srs_global_indices" title="from remote sensing data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Compute biodiversity indices</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=srs_metadata" title="metadata documents"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Validate ISO 19139</button></a>
+<h3 id="speciesabundance">Species abundance</h3>
+<a href="https://usegalaxy.eu/root?tool_id=pampa_glmsp" title="Compute a GLM of your choice on population data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Compute GLM on population data</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=pampa_glmcomm" title="Compute a GLM of your choice on community data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Compute GLM on community data</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=stoceps_trend_indic" title="using GlmmTMB or GAM models"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Temporal trend indicator</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=stoceps_glm_group" title="by specialization group"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Estimate temporal population variation</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=stoceps_glm" title="by species"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Estimate temporal population variation</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=stoceps_filteringsp" title="with rare and low abundances"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Filter species</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=stoceps_maketablecarrer" title="for evolution trend analyzes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Preprocess population data</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=xarray_metadata_info" title="summarize content of a Netcdf file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NetCDF xarray Metadata Info</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=xarray_select" title="extracts variable values with custom conditions on dimensions"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NetCDF xarray Selection</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=pampa_communitymetrics" title="calculate community metrics from abundance data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Calculate community metrics</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=pampa_presabs" title="calculate presence absence table from observation data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Calculate presence absence table</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=pampa_plotglm" title="as temporal trend"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Create a plot from GLM data</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=regionalgam_gls" title="with a simple linear regression"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Model temporal trend</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=regionalgam_flight_curve" title="compute the regional expected pattern of abundance"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Flight curve</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=regionalgam_autocor_acf" title="check for temporal autocorrelation in the residuals"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Autocorrelation test</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=regionalgam_glmmpql" title="of species abundance"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Expected temporal trend</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=regionalgam_gls_adjusted" title="for autocorrelation in the residuals"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Linear regression ajusted</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=regionalgam_plot_trend" title="with trend line"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Plot abundance</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=regionalgam_ab_index" title="computation across species, sites and years"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Abundance index</button></a>
+<h3 id="computeindicatorsforturnoverbouldersfields">Compute indicators for turnover boulders fields</h3>
+<a href="https://usegalaxy.eu/root?tool_id=cb_dissim" title="indicator"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">QECB-Dissimilarity</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cb_ivr" title="indicator"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">IVR</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cb_div" title="indicators"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Diversity</button></a>
+<h3 id="gisdatahandling">GIS Data Handling</h3>
+<a href="https://usegalaxy.eu/root?tool_id=ccds_download_era5_af" title="Download ERA5 data from the Copernicus Climate Data Store to provide as input to the AquaINFRA marine model. Products: ERA5 hourly data on single levels from 1940 to present, Reanalysis."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Copernicus CDS Downloader for AquaINFRA marine model</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cmems_download_ic_bc" title="Download data from the Copernicus Marine Service to provide as input to the AquaINFRA marine model. Products: Mediterranean Sea Physics Analysis and Forecast or Mediterranean Sea Physics Reanalysis, depending on the selected temporal period."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Copernicus CMEMS Downloader for AquaINFRA marine model</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=3dtrees_py3dtiles" title="Convert LAS/LAZ collection to Cesium 3D points_tiles"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">3Dtrees: Py3DTiles Converter</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=3dtrees_overviews" title="Generate 3D point cloud overview images from LAZ/LAS datasets"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">3Dtrees: Overviews</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=3dtrees_standardization" title="Standardize LAS/LAZ files or validate collections for consistency"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">3DTrees: LAS/LAZ Standardization</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=3dtrees_tile_merge" title="Subsampling, tiling, merging and matching of point clouds"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">3Dtrees: Tile and Merge</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=xarray_metadata_info" title="summarize content of a Netcdf file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NetCDF xarray Metadata Info</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=xarray_select" title="extracts variable values with custom conditions on dimensions"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NetCDF xarray Selection</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=gdal_ogrinfo" title="lists information about an OGR supported data source"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">OGR Informations</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=gdal_ogr2ogr" title="converts simple features data between file formats"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">OGR2ogr</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=gdal_gdalwarp" title="image reprojection and warping utility"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GDAL Warp</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=gdal_gdal_translate" title="converts raster data between different formats."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GDAL Translate</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=gdal_gdal_merge" title="mosaics a set of images"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GDAL Merge</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=gdal_gdalinfo" title="lists information about a raster dataset"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GDAL Informations</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=gdal_gdalbuildvrt" title="builds a VRT from a list of datasets"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GDAL Build VRT</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=gdal_gdaladdo" title="builds or rebuilds overview images"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GDAL addo</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=xarray_netcdf2netcdf" title="manipulate xarray from netCDF and save back to netCDF"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NetCDF xarray operations</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=xarray_mapplot" title="Visualize netCDF variables on a geographical map"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NetCDF xarray map plotting</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=xarray_coords_info" title="Get values for each coordinate of a Netcdf file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NetCDF xarray Coordinate Info</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=interpolation_run_idw_interpolation" title="based on Inverse Distance Weighting (IDW)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Run interpolation</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=otb_band_math" title="outputs a monoband image as a result of a mathematical operation on several multi-band images"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">OTB.BandMath</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=otb_mean_shift_smoothing" title="smooths an image using the MeanShift algorithm"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">OTB.MeanShiftSmoothing</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=terrabyte_ogc_api_processes" title="Water quality EO Application Package"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Terrabyte OGC API Processes</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=zoo_project_ogc_api_processes" title="executes remote OTB processes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Zoo Project OGC API Processes</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=hirondelle_crim" title="executes remote processes."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Hirondelle CRIM OGC API Processes</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=aquainfra_ogc_api_processes" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">AquaINFRA OGC API Processes</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=3dtrees_detailview" title="species prediction on segmented point cloud."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">3Dtrees: DetailView</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=3dtrees_segmentanytree" title="Forest instance segmentation."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">3Dtrees: SegmentAnyTree</button></a>
+<h3 id="climateanalysis">Climate Analysis</h3>
+<a href="https://usegalaxy.eu/root?tool_id=ctsm_fates" title="Functionally Assembled Terrestrial Ecosystem Simulator"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CTSM/FATES-EMERALD</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=climate_stripes" title="from timeseries"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">climate stripes</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=psy_maps" title="gridded (lat/lon) netCDF data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">map plot</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cds_essential_variability" title="for assessing climate variability"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Copernicus Essential Climate Variables</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=mean_per_zone" title="over each area"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">zonal statistics</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=shyft_longitudes" title="from netCDF data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">shift longitudes</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=c3s" title="for retrieving climate data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Copernicus Climate Data Store</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cesm" title="Community Earth System Model"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CESM</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cads" title="for retrieving data from the Atmosphere Monitoring Service"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Copernicus Atmosphere Data Store</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=eodie" title="converts simple features data between file formats"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">EODIE</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cdo_operations" title="Climate Data Manipulation Operators operations for standard processing of climate and NWP model output."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CDO Operations</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cdo_info" title="Climate Data Information Operators to get information on Climate and NWP model data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CDO get info</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=timeseries_extraction" title="Extract and plot time series"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NetCDF timeseries Extractor</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=landcover_subindicator" title="subindicator to track land changes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Land cover degradation</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=harmonize_insitu_to_netcdf" title="and aggregator of in-situ marine physical and biogeochemical data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">QCV harmonizer</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=tool_odv" title="tool for qualificiation and validation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ODV collection manager</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bgc_canyon_b" title="estimation of ocean CO2 variables and nutrient concentrations"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Canyon-B</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=tool_odv_history" title="reports user action performed with ODV"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ODV history manager</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=tool_biogeochemical_calibration" title="for sensors according to Argo recommendations"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BioGeoChemical calibration</button></a>
+<h3 id="biodiversitydataexploration">Biodiversity data exploration</h3>
+<a href="https://usegalaxy.eu/root?tool_id=tool_anonymization" title="without loss of the spatial relationships"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Spatial coordinates anonymization</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ecology_beta_diversity" title="Computes a measure of beta diversity, SCBD and representations"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Local Contributions to Beta Diversity (LCBD)</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ecology_homogeneity_normality" title="Checks the homogeneity of the variance and the normality of the distribution"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Homoscedasticity and normality</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ecology_link_between_var" title="Shows interaction, correlation, colinearity, produces a PCA and computes VIF for biodiversity abundance data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Variables exploration</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ecology_presence_abs_abund" title="Community abundance map, presence barplot and rarefaction curves"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Presence-absence and abundance</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ecology_stat_presence_abs" title="of a numeric variable"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Statistics on presence-absence</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cb_div" title="indicators"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Diversity</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=obisindicators" title="from OBIS"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Ocean biodiversity indicators</button></a>
+<h3 id="dataandmetadatamanagement">Data and Metadata Management</h3>
+<a href="https://usegalaxy.eu/root?tool_id=makeeml" title="Create EML from EAL templates"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Make EML</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=eml2eal" title="Create EAL templates from EML metadata"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">EML to EAL</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=eal_templates" title="for core features of a data package for EML metadata creation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Make templates</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=eal_table_template" title="attributes and categorical variables for EML metadata creation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Make templates for data tables</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=geo_cov_template" title="for EML metadata creation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Make geographic coverage template</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=taxo_cov_template" title="for EML metadata creation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Make taxonomic coverage template</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=raster_template" title="attributes for EML metadata creation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Make templates for raster files</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=vector_template" title="attributes for EML metadata creation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Make templates for vector files</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=entities_template" title="for EML metadata creation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Make entities templates for raster, vector and other entities files</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=annotations_template" title="from scratch or from EML metadata file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Make annotations template</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=eml_validate" title="check if your EML file is valid"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Eml validate:</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=data_paper_from_EML" title="from EML"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Make data paper sketches</button></a>
 <hr/><h2 id="miscellaneoustools">Miscellaneous Tools</h2>
 <h3 id="evolution">Evolution</h3>
-<a href="https://usegalaxy.eu/root?tool_id=revoluzer_crex" title="reconstruct pairwise gene order rearrangement"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CREx</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=iqtree" title="Phylogenomic / evolutionary tree construction from multiple sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">IQ-TREE</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=mutate_snp_codon_1" title="with SNPs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Mutate Codons</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=iqtree" title="Phylogenomic / evolutionary tree construction from multiple sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">IQ-TREE</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=codeml" title="Detects positive selection (paml package)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">codeML</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=structure" title="using multi-locus genotype data to investigate population structure"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Structure</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=rapidnj" title="rapidly with RapidNJ"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Join neighbors</button></a>
@@ -3143,8 +3337,10 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=tn93_filter" title="- remove sequences from a reference that are within a given distance of of a cluster"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">TN93 Filter</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=tn93_cluster" title="sequences that lie within a specific distance of each other"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">TN93 Cluster</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=tn93_readreduce" title="into clusters with TN-93"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Merge matching reads</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=revoluzer_crex" title="reconstruct pairwise gene order rearrangement"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CREx</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=revoluzer_distmat" title="for gene orders"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Compute distance matrix</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=quicktree" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Quicktree</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=map_damage" title="Tracks and quantifies damage patterns in ancient DNA sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">mapDamage</button></a>
 <h3 id="motiftools">Motif Tools</h3>
 <a href="https://usegalaxy.eu/root?tool_id=rgweblogo3" title="generator for fasta (eg Clustal alignments)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Sequence Logo</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=meme_psp_gen" title="- perform discriminative motif discovery"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MEME psp-gen</button></a>
@@ -3152,13 +3348,27 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=meme_meme" title="- Multiple EM for Motif Elicitation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MEME</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=meme_dreme" title="- Discriminative Regular Expression Motif Elicitation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">DREME</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=meme_chip" title="- motif discovery, enrichment analysis and clustering on large nucleotide datasets"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MEME-ChIP</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=meme_streme" title="Simple, Thorough, Rapid, Enriched Motif Elicitation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">STREME</button></a>
 <h3 id="testtools">Test Tools</h3>
-<a href="https://usegalaxy.eu/root?tool_id=quality_script_fastp_bracken" title="Quality control using FastP and Bracken"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Quality Control FastP Bracken</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=quast_get_fasta" title="Extracts QUAST metrics and generates FASTA files from JSON input."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">QUAST Analysis and FASTA Generator</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=mlst_amr_staramr" title="Extracts MLST, AMRfinder Plus, and STARamr results from JSON input."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MLST, AMRfinder, and STARamr Analysis</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=mfa_align" title="align a corpus using an acoustic model and dictionary"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MFA Align</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=mfa_g2p" title="generate a pronunciation dictionary from a word list or corpus"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MFA G2P</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=mfa_tokenize" title="split text into words using a tokenizer model (e.g., for Japanese/Chinese)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MFA Tokenize</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=mfa_train_dictionary" title="calculate pronunciation probabilities for a dictionary"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MFA Train Dictionary</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=mfa_train_lm" title="train a language model (N-gram) from a text corpus"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MFA Train LM</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=mfa_validate" title="validate a corpus and dictionary for alignment"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MFA Validate</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=mfa_adapt" title="adapt a pretrained acoustic model to a new dataset"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MFA Adapt</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=mfa_find_oovs" title="find words in a corpus that are missing from the dictionary"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MFA Find OOVs</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=mfa_remap_alignments" title="convert TextGrid transcriptions to a new phone set"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MFA Remap Alignments</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=mfa_train" title="train a new acoustic model from a corpus"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MFA Train</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=mfa_train_g2p" title="train a new G2P model from a pronunciation dictionary"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MFA Train G2P</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=mfa_train_tokenizer" title="train a tokenizer model from a corpus and dictionary"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MFA Train Tokenizer</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=mfa_validate_dictionary" title="check a pronunciation dictionary for formatting errors"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MFA Validate Dictionary</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=chipeakanno_annopeaks" title="annotate peaks by annoGR object in the given range"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ChIPpeakAnno annoPeaks</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=clusterprofiler_bitr" title="converting ID types"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Cluster Profiler Bitr</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=clusterprofiler_go" title="run GO Analysis"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Cluster Profiler GO</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=quality_script_fastp_bracken" title="Quality control using FastP and Bracken"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Quality Control FastP Bracken</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=quast_get_fasta" title="Extracts QUAST metrics and generates FASTA files from JSON input."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">QUAST Analysis and FASTA Generator</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=mlst_amr_staramr" title="Extracts MLST, AMRfinder Plus, and STARamr results from JSON input."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">MLST, AMRfinder, and STARamr Analysis</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=netcdf2zarr" title="Rewrite a netCDF to Zarr"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NetCDF to Zarr</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=interactive_zeppelin_notebook" title="Zeppelin Notebook"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">zeppelin</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=concatenate_icenet_data" title="for concatenating yearly sea ice concentration netcdf files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Concatenate Icenet Data</button></a>
@@ -3174,53 +3384,18 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=tombo_plot_most_significant" title="Plotting amperage signal at the locations deemed most significant by the tombo"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Tombo plot most signficant</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=tombo_plot_genome_locations" title="Plotting amperage signal from nanopore reads at the locations specified"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Tombo plot genome locations</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=proteomics_search_peptide_prophet_1" title="Calculate Peptide Prophet statistics on search results"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Peptide Prophet</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=proteomics_search_protein_prophet_1" title="Calculate Protein Prophet statistics on search results"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Protein Prophet</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=proteomics_search_interprophet_1" title="Combine Peptide Prophet results from multiple search engines"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">InterProphet</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bwtool-lift" title="Project data base-by-base into a new assembly using a liftOver chain file from UCSC"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bwtool-lift</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bg_protein_properties" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Calculate protein properties</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=biopython_base_distribution" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Base Count</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=codon_count" title="gives numbers of all different codons in the whole sequence"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Codon count</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=genbank_to_gff" title="to GFF converter"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GenBank and EBML</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=gbk_to_orf" title="files (CDS, gene ...)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Extract sequences from GenBank</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=gff_to_sequence" title="to GenBank or embl"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GFF converter</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=sequence_convert" title="for various sequence formats"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Sequence converter</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=translate_nucleotides" title="to amino acids"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Translate nucleotides</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=rnalfoldz" title="calculates locally stable secondary structures of RNA"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RNALfoldz</button></a>
-<h3 id="gisdatahandling">GIS Data Handling</h3>
-<a href="https://usegalaxy.eu/root?tool_id=aquainfra_ogc_api_processes" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">AquaINFRA OGC API Processes</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=xarray_metadata_info" title="summarize content of a Netcdf file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NetCDF xarray Metadata Info</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=xarray_select" title="extracts variable values with custom conditions on dimensions"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NetCDF xarray Selection</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=gdal_ogrinfo" title="lists information about an OGR supported data source"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">OGR Informations</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=gdal_ogr2ogr" title="converts simple features data between file formats"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">OGR2ogr</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=gdal_gdalwarp" title="image reprojection and warping utility"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GDAL Warp</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=gdal_gdal_translate" title="converts raster data between different formats."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GDAL Translate</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=gdal_gdal_merge" title="mosaics a set of images"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GDAL Merge</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=gdal_gdalinfo" title="lists information about a raster dataset"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GDAL Informations</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=gdal_gdalbuildvrt" title="builds a VRT from a list of datasets"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GDAL Build VRT</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=gdal_gdaladdo" title="builds or rebuilds overview images"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GDAL addo</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=xarray_netcdf2netcdf" title="manipulate xarray from netCDF and save back to netCDF"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NetCDF xarray operations</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=xarray_mapplot" title="Visualize netCDF variables on a geographical map"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NetCDF xarray map plotting</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=xarray_coords_info" title="Get values for each coordinate of a Netcdf file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NetCDF xarray Coordinate Info</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=interpolation_run_idw_interpolation" title="based on Inverse Distance Weighting (IDW)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Run interpolation</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=otb_band_math" title="outputs a monoband image as a result of a mathematical operation on several multi-band images"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">OTB.BandMath</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=otb_mean_shift_smoothing" title="smooths an image using the MeanShift algorithm"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">OTB.MeanShiftSmoothing</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=terrabyte_ogc_api_processes" title="Water quality EO Application Package"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Terrabyte OGC API Processes</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=zoo_project_ogc_api_processes" title="executes remote OTB processes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Zoo Project OGC API Processes</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=hirondelle_crim" title="executes remote processes."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Hirondelle CRIM OGC API Processes</button></a>
-<h3 id="animaldetectiononacousticrecordings">Animal Detection on Acoustic Recordings</h3>
-<a href="https://usegalaxy.eu/root?tool_id=spocc_occ" title="from GBIF, ALA, iNAT and others"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Get species occurrences data</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=vigiechiro_bilanenrichipf" title="from Animal Detection on Acoustic Recordings"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Advanced restitution: 'Point fixe' protocol</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=vigiechiro_bilanenrichirp" title="from Animal Detection on Acoustic Recordings"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Advanced restitution: 'Routier'or 'Pedestre' protocols</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=vigiechiro_idcorrect_2ndlayer" title="clean data from animal detection on acoustic recordings"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Tadarida data cleaner</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=vigiechiro_idvalid" title="Integrate identifications from animal detection on acoustic recordings"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Tadarida identifications validation</button></a>
-<h3 id="computeindicatorsforsatelliteremotesensing">Compute indicators for satellite remote sensing</h3>
-<a href="https://usegalaxy.eu/root?tool_id=srs_pca" title="from remote sensing data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Compute a PCA raster</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=srs_diversity_maps" title="from remote sensing data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Map diversity</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=srs_preprocess_s2" title="read, crop, resample and write it as a raster stack"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Preprocess sentinel 2 data</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=srs_spectral_indices" title="as NDVI from remote sensing data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Compute spectral indices</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=srs_process_data" title="with remote sensing data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Compare diversity indicators</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=srs_global_indices" title="from remote sensing data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Compute biodiversity indices</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=srs_metadata" title="metadata documents"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Validate ISO 19139</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=proteomics_search_protein_prophet_1" title="Calculate Protein Prophet statistics on search results"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Protein Prophet</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=proteomics_search_interprophet_1" title="Combine Peptide Prophet results from multiple search engines"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">InterProphet</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bwtool-lift" title="Project data base-by-base into a new assembly using a liftOver chain file from UCSC"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bwtool-lift</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bg_protein_properties" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Calculate protein properties</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=biopython_base_distribution" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Base Count</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=codon_count" title="gives numbers of all different codons in the whole sequence"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Codon count</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=genbank_to_gff" title="to GFF converter"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GenBank and EBML</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=gbk_to_orf" title="files (CDS, gene ...)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Extract sequences from GenBank</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=gff_to_sequence" title="to GenBank or embl"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GFF converter</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=sequence_convert" title="for various sequence formats"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Sequence converter</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=translate_nucleotides" title="to amino acids"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Translate nucleotides</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=rnalfoldz" title="calculates locally stable secondary structures of RNA"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RNALfoldz</button></a>
 <h3 id="regionalvariation">Regional Variation</h3>
 <a href="https://usegalaxy.eu/root?tool_id=indels_3way" title="from 3-way alignments"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Fetch Indels</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=draw_stacked_barplots" title="for different categories and different criteria"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Draw Stacked Bar Plots</button></a>
@@ -3269,30 +3444,10 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=gd_rank_terms" title=": Assess the enrichment/depletion of a gene set for GO terms"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Rank Terms</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=gd_new_oscar" title=": Look up KEGG pathways for given Ensembl transcripts"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Get Pathways</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=gd_cluster_kegg" title=": Group gene categories connected by shared genes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Cluster KEGG</button></a>
-<h3 id="climateanalysis">Climate Analysis</h3>
-<a href="https://usegalaxy.eu/root?tool_id=harmonize_insitu_to_netcdf" title="and aggregator of in-situ marine physical and biogeochemical data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">QCV harmonizer</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=tool_odv" title="tool for qualificiation and validation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ODV collection manager</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=tool_odv_history" title="reports user action performed with ODV"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ODV history manager</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bgc_canyon_b" title="estimation of ocean CO2 variables and nutrient concentrations"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Canyon-B</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ctsm_fates" title="Functionally Assembled Terrestrial Ecosystem Simulator"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CTSM/FATES-EMERALD</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=climate_stripes" title="from timeseries"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">climate stripes</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=psy_maps" title="gridded (lat/lon) netCDF data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">map plot</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=cds_essential_variability" title="for assessing climate variability"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Copernicus Essential Climate Variables</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=mean_per_zone" title="over each area"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">zonal statistics</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=shyft_longitudes" title="from netCDF data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">shift longitudes</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=c3s" title="for retrieving climate data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Copernicus Climate Data Store</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=cesm" title="Community Earth System Model"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CESM</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=cads" title="for retrieving data from the Atmosphere Monitoring Service"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Copernicus Atmosphere Data Store</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=eodie" title="converts simple features data between file formats"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">EODIE</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=cdo_operations" title="Climate Data Manipulation Operators operations for standard processing of climate and NWP model output."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CDO Operations</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=cdo_info" title="Climate Data Information Operators to get information on Climate and NWP model data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CDO get info</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=tool_biogeochemical_calibration" title="for sensors according to Argo recommendations"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BioGeoChemical calibration</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=timeseries_extraction" title="Extract and plot time series"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NetCDF timeseries Extractor</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=landcover_subindicator" title="subindicator to track land changes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Land cover degradation</button></a>
 <h3 id="apollo">Apollo</h3>
-<a href="https://usegalaxy.eu/root?tool_id=list_organism" title="in Apollo"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">List Organisms</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=create_account" title="with Apollo"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Register Account</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=iframe" title="opens an IFrame to Apollo"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Annotate</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=list_organism" title="in Apollo"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">List Organisms</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=fetch_jbrowse" title="for an organism, from Apollo"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Retrieve JBrowse</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=feat_from_gff3" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GFF3 to Apollo Annotations</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=export" title="from Apollo into Galaxy"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Retrieve Data</button></a>
@@ -3300,15 +3455,11 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=delete_organism" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Delete an Apollo record</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=delete_features" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Delete all annotations from an Apollo record</button></a>
 <h3 id="imaging">Imaging</h3>
-<a href="https://usegalaxy.eu/root?tool_id=doclayoutyolo" title="Enhancing document layout analysis"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">DocLayout-YOLO</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=vitessce_spatial" title="Visual Integration Tool for the Exploration of Spatial Single-Cell Experiments"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Vitessce</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=tesseract" title="Optical Character Recognition"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Tesseract</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=libcarna_render" title="with LibCarna"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Render 3-D image data</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ip_crop_image" title="with giatools"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Crop image</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ip_binary_to_labelimage" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert binary image to label map</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bia_download" title="Download images from Bioimage Archive"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FTP Link for Bioimage Archive</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ip_points_to_label" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert coordinates to label map</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bioimage_inference" title="with PyTorch"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Process image using a BioImage.IO model</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=cellpose" title="with Cellpose"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Run generalist cell and nucleus segmentation</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=omero_filter" title="with ezomero"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">OMERO IDs</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=clip_image" title="with giatools"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Clip image intensities</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ridge_filter_skimage" title="with scikit-image"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Apply ridge filter</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=cp_cellprofiler" title="with CellProfiler 3"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Run CellProfiler pipeline</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=cp_common" title="Load images and metadata"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Starting Modules</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=cp_color_to_gray" title="with CellProfiler"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ColorToGray</button></a>
@@ -3374,12 +3525,14 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=ip_2d_feature_extraction" title="with scikit-image"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Extract image features</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ip_permutate_axis" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Permutate image axes</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ip_labelimage_to_points" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert label map to points (center of masses)</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ip_points_to_label" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert coordinates to label map</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ip_concat_channels" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Concatenate images or channels</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ip_scale_image" title="with scikit-image"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Scale image</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ip_merge_neighbours_in_label" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Merge neighbors in label map</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ip_2d_filter_segmentation_by_features" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Filter label map by rules</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ip_binary_to_labelimage" title="with giatools"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert binary image to label map</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ip_2d_filter_segmentation_by_features" title="with giatools"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Filter label map by rules</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ip_anisotropic_diffusion" title="with MedPy"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Apply anisotropic diffusion</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ip_filter_standard" title="with scipy"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Filter 2-D image</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ip_filter_standard" title="with scipy"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Apply standard image filter</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=imagecoordinates_flipaxis" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Switch axis coordinates</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ip_coordinates_of_roi" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert binary image to points (point coordinates)</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ip_count_objects" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Count objects in label map</button></a>
@@ -3389,6 +3542,9 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=ip_binaryimage_to_points" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert binary image to points (center of masses)</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ip_slice_image" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Slice image into patches</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ip_split_labelmap" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Split label map using morphological operators</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=json2yolosegment" title="with ultralytics"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert AnyLabeling JSON to YOLO text</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=yolo_predict" title="with ultralytics"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Perform YOLO image labeling</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=yolo_training" title="with ultralytics"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Perform YOLO training</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=background_removal" title="with scikit-image"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Remove image background</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ip_colocalization" title="of two segmentation maps"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Colocalization</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ip_viz_overlay_moving_and_fixed_image" title="moving and fixed image"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Overlay</button></a>
@@ -3401,74 +3557,44 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=cp_cellprofiler4" title="with CellProfiler 4"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Run CellProfiler pipeline</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ip_segmetrics" title="with SegMetrics"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Compute image segmentation and object detection performance measures</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=gate_finder" title="with Vitessce"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Perform gating</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=squidpy_spatial" title="with Squidpy"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Analyze and visualize spatial multi-omics data</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=vitessce_spatial" title="Visual Integration Tool for the Exploration of Spatial Single-Cell Experiments"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Vitessce</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=rename_tiff_channels" title="with ome-types"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Rename OME-TIFF channels</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=cell_intensity_processing" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Process single-cell intensities</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ip_superdsm" title="with SuperDSM"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Perform segmentation using deformable shape models</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=rfove" title="with RFOVE"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Perform segmentation using region-based fitting of overlapping ellipses</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=omero_get_id" title="with ezomero"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">OMERO get IDs</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=omero_get_value" title="with ezomero"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">OMERO get Object</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ip_color_deconvolution" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Perform color deconvolution or transformation</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ip_split_image" title="with NumPy"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Split image along axes</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bia_download" title="Download images from Bioimage Archive"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FTP Link for Bioimage Archive</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=woundhealing_scratch_assay" title="image analysis"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Wound healing scratch assay</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=yolo_predict" title="with ultralytics"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Perform YOLO image labeling</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=scimap_anndata_to_csv" title="with Scimap"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert Anndata to CSV</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=yolo_training" title="with ultralytics"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Perform YOLO training</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bf2raw" title="with Bioformats"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert to OME-Zarr</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cellpose" title="with Cellpose 3"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Run generalist cell and nucleus segmentation</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bf2raw" title="with Bio-Formats"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert to OME-Zarr</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=voronoi_tessellation" title="with scikit-image"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Compute Voronoi tessellation</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=morphological_operations" title="with SciPy"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Apply a morphological operation</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=image_math" title="with NumPy"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Process images using arithmetic expressions</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=orientationpy" title="with OrientationPy"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Compute image orientation</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=label_to_binary" title="with NumPy"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert label map to binary image</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=colorize_labels" title="with NetworkX"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Colorize label map</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=cellposesam" title="with Cellpose-SAM"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Run generalist cell and nucleus segmentation</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=repeat_channels" title="with NumPy"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert single-channel to multi-channel image</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=squidpy_scatter" title="with Squidpy"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Create spatial scatterplot</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=squidpy_spatial" title="with Squidpy"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Analyze and visualize spatial multi-omics data</button></a>
-<h3 id="speciesabundance">Species abundance</h3>
-<a href="https://usegalaxy.eu/root?tool_id=pampa_glmsp" title="Compute a GLM of your choice on population data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Compute GLM on population data</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=pampa_glmcomm" title="Compute a GLM of your choice on community data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Compute GLM on community data</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=stoceps_trend_indic" title="using GlmmTMB or GAM models"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Temporal trend indicator</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=stoceps_glm_group" title="by specialization group"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Estimate temporal population variation</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=stoceps_glm" title="by species"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Estimate temporal population variation</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=stoceps_filteringsp" title="with rare and low abundances"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Filter species</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=stoceps_maketablecarrer" title="for evolution trend analyzes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Preprocess population data</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=xarray_metadata_info" title="summarize content of a Netcdf file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NetCDF xarray Metadata Info</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=xarray_select" title="extracts variable values with custom conditions on dimensions"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NetCDF xarray Selection</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=pampa_communitymetrics" title="calculate community metrics from abundance data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Calculate community metrics</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=pampa_presabs" title="calculate presence absence table from observation data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Calculate presence absence table</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=pampa_plotglm" title="as temporal trend"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Create a plot from GLM data</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=regionalgam_gls" title="with a simple linear regression"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Model temporal trend</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=regionalgam_flight_curve" title="compute the regional expected pattern of abundance"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Flight curve</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=regionalgam_autocor_acf" title="check for temporal autocorrelation in the residuals"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Autocorrelation test</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=regionalgam_glmmpql" title="of species abundance"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Expected temporal trend</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=regionalgam_gls_adjusted" title="for autocorrelation in the residuals"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Linear regression ajusted</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=regionalgam_plot_trend" title="with trend line"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Plot abundance</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=regionalgam_ab_index" title="computation across species, sites and years"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Abundance index</button></a>
-<h3 id="computeindicatorsforturnoverbouldersfields">Compute indicators for turnover boulders fields</h3>
-<a href="https://usegalaxy.eu/root?tool_id=cb_dissim" title="indicator"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">QECB-Dissimilarity</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=cb_ivr" title="indicator"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">IVR</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=cb_div" title="indicators"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Diversity</button></a>
-<h3 id="ecoregionalization">Ecoregionalization</h3>
-<a href="https://usegalaxy.eu/root?tool_id=ecoregion_eco_map" title="Create map from cluster to visualize ecoregions"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">EcoMap</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ecoregion_brt_analysis" title="for species distribution modelling"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BRT tool prediction</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ecoregion_taxa_seeker" title="for recover list of taxa"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">TaxaSeeker</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ecoregion_cluster_estimate" title="Find an optimal number of cluster with SIH index"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ClusterEstimate</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ecoregion_clara_cluster" title="Make cluster from BRT prediction with Clara algorithm"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ClaraClust</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ecoregion_GeoNearestNeighbor" title="Merge two data tables by finding the closest points based on latitude and longitude coordinates (WGS84 projection)."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GeoNearestNeighbor</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ClaraGuess" title="Environmental clustering using CLARA and BRT predictions"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Clara Estimate and Clustering</button></a>
-<h3 id="indicatorsfromgeometricmean">Indicators from geometric mean</h3>
-<a href="https://usegalaxy.eu/root?tool_id=Map_shp" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Make a map with a shapefile</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=Mean_geom" title="- calcul of the geometric means for the 'bois mort' indicator"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Geometric means</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bar_plot" title="for simple discrete data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Bar plot</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=divand_full_analysis" title="Data-Interpolating Variational Analysis in n dimensions"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">DIVAnd</button></a>
-<h3 id="phylodiversity">Phylodiversity</h3>
-<a href="https://usegalaxy.eu/root?tool_id=crsconverter" title="from environmental predictors for species distribution modeling"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CRSconverter</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=phylo_index" title="compute phylodiversity index based on matched phylogenetic and occupancy data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PhyloIndex</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=phylogenetic_occupancy_matcher" title="match phylogenetic and occupancy data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PhylOccuMatcher</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=estimate_endem" title="of each cell of a spatial grid"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">EstimEndem</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=scimap_anndata_to_csv" title="with Scimap"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert Anndata to CSV</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bioimage_inference" title="with PyTorch"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Process image using a BioImage.IO model</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ip_color_deconvolution" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Perform color deconvolution or transformation</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=omero_filter" title="with ezomero"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">OMERO IDs</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=omero_get_id" title="with ezomero"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">OMERO get IDs</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=omero_get_value" title="with ezomero"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">OMERO get Object</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ip_split_image" title="with NumPy"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Split image along axes</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=doclayoutyolo" title="Enhancing document layout analysis"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">DocLayout-YOLO</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=pdfimages" title="Extract images from a PDF file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">pdfimages</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=biapy" title="Accessible deep learning on bioimages"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Build a workflow with BiaPy</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=imagemagick_image_montage" title="with ImageMagick"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Image Montage</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=iscc_sum" title="with ISCC-SUM"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Generate ISCC-CODE</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=iscc_sum_verify" title="with ISCC-SUM"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Verify ISCC-CODE</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=iscc_sum_similarity" title="with ISCC-SUM"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Find datasets with similar ISCC-CODEs</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=highdicom_dicom2text" title="with highdicom"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Export DICOM metadata</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=highdicom_dicom2tiff" title="with highdicom"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert DICOM to TIFF</button></a>
 <h3 id="astronomy">Astronomy</h3>
-<a href="https://usegalaxy.eu/root?tool_id=astropy_fits2csv" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">astropy fits2csv</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=astropy_fits2bitmap" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">astropy fits2bitmap</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=astropy_fits2csv" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">astropy fits2csv</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=astropy_fitsinfo" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">astropy fitsinfo</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=astronomical_archives" title="queries astronomical archives through Virtual Observatory protocols"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Astronomical Archives (IVOA)</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=sgwb_astro_tool" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SGWB</button></a>
@@ -3479,10 +3605,15 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=desi_legacy_survey_astro_tool" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">DESI Legacy Survey</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=plot_tools_astro_tool" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Plot Tools</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=analyse_short_astro_text_astro_tool" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">analyse-short-astro-text</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=fits2tiff_astro_tool" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">fits2tiff</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=source_extractor_astro_tool" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">source-extractor</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=grb_detection_astro_tool" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GRB detection</button></a>
 <h3 id="interactivetools">Interactive tools</h3>
 <a href="https://usegalaxy.eu/root?tool_id=interactive_tool_source" title="Sea Observations Utility for Reprocessing, Calibration and Evaluation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Interactive Source Notebooks</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=interactive_tool_cellxgene_mouse_sciatic_nerve" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Interactive Mouse Sciatic Nerve CellxGene Environment</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=interactive_tool_napari" title="interactive tool"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Run Napari</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=interactive_tool_anylabeling" title="Effortless data labeling with AI support from YOLO and Segment Anything!"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">AnyLabeling Interactive</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=interactive_tool_pretextview" title="Paired REad TEXTure Viewer Contact Map Viewer"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PretextView</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=interactive_tool_bellavista" title="Visualization for Imaging-Based Spatial Transcriptomics"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">BellaVista Interactive</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=interactive_tool_cellprofiler" title="interactive tool"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Run CellProfiler</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=interactive_tool_tadviewer" title="interactive table viewer with SQL enginer for filtering"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">tadviewer</button></a>
@@ -3501,31 +3632,30 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=interactive_tool_pavian" title="Interactive analysis of metagenomics data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Pavian</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=interactive_tool_pcstudio" title="Interactive tool to create, simulate, and visualize a multicellular model using PhysiCell"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PhysiCell Studio</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=interactive_tool_copasi" title="Biochemical System Simulator"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">COPASI</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=interactive_tool_mgnify_notebook" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Interactive MGnify Notebook</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=interactive_tool_libertem" title="Open Pixelated STEM platform"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">LiberTEM</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=interactive_tool_mgnify_notebook" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Interactive MGnify Notebook</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=interactive_tool_jupyter_notebook" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Interactive JupyterLab Notebook</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=interactive_tool_jupytergis_notebook" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Interactive JupyterGIS Notebook</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=interactive_tool_ml_jupyter_notebook" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GPU-enabled Interactive Jupyter Notebook for Machine Learning</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=interactive_tool_climate_notebook" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Interactive Climate Notebook</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=interactive_tool_jupytergis_notebook" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Interactive JupyterGIS Notebook</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=interactive_tool_pangeo_notebook" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Interactive Pangeo Notebook</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=interactive_tool_pangeo_ml_notebook" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Interactive Pangeo Machine Learning Notebook</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=interactive_tool_cellpose" title="a generalist algorithm for cellular segmentation and restoration"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">CellPose Interactive</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=interactive_tool_rstudio" title="R 4.4.2 with Bioconductor 3.20"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RStudio</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=interactive_tool_pyiron" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">PyIron Interactive Jupyter Notebook</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=interactive_tool_higlass" title="an interactive Hi-C data visualizer."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">HiGlass</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=interactive_tool_openrefine" title="Working with messy data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">OpenRefine</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=interactive_tool_panoply" title="interative plotting tool for geo-referenced data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Panoply</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=interactive_tool_askomics" title="a visual SPARQL query builder"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">AskOmics</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=interactive_tool_cellxgene" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Interactive CELLxGENE Environment</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=interactive_tool_cellxgene_vip" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Interactive CELLxGENE VIP Environment</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=interactive_tool_bam_iobio" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bam.iobio visualisation</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=interactive_tool_vcf_iobio" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">VCF (iobio) Visualisation</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=interactive_tool_neo4j" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Neo4j (Graph Database)</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=interactive_tool_openrefine" title="Working with messy data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">OpenRefine</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=interactive_tool_escriptorium" title="interactive tool"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Run eScriptorium</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=interactive_tool_phinch" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Phinch Visualisation</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=interactive_tool_paraview" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Paraview</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=interactive_tool_wilson" title="Webbased Interactive Omics visualization"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Wilson</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=interactive_tool_wallace" title="Webbased Interactive modeling of species niches and distributions"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Wallace</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=interactive_tool_cellxgene_vip" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Interactive CELLxGENE VIP Environment</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=interactive_tool_geoexplorer" title="An interactive spatial analysis platform using ggvis and Leaflet"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">geoexplorer</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=interactive_tool_radiant" title="Data analytics using Radiant R Shiny app"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">radiant</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=interactive_tool_ethercalc" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">EtherCalc</button></a>
@@ -3560,25 +3690,10 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=onto_tk_get_root_terms" title="of a given OBO term"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Get the root terms</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=onto_tk_get_relationship_id_vs_relationship_name" title="from the given OBO ontology"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Get all the relationship IDs and names</button></a>
 <h3 id="hca-singlecell">HCA-Single Cell</h3>
-<a href="https://usegalaxy.eu/root?tool_id=scanpy_find_markers" title="to find differentially expressed genes between groups"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Scanpy FindMarkers</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=scanpy_scale_data" title="to make expression variance the same for all genes"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Scanpy ScaleData</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=scanpy_run_umap" title="visualise cell clusters using UMAP"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Scanpy RunUMAP</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=scanpy_run_tsne" title="visualise cell clusters using tSNE"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Scanpy RunTSNE</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=scanpy_run_pca" title="for dimensionality reduction"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Scanpy RunPCA</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=scanpy_read_10x" title="into hdf5 object handled by scanpy"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Scanpy Read10x</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=scanpy_normalise_data" title="to make all cells having the same total expression"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Scanpy NormaliseData</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=scanpy_find_variable_genes" title="based on normalised dispersion of expression"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Scanpy FindVariableGenes</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=scanpy_find_cluster" title="based on community detection on KNN graph"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Scanpy FindCluster</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=scanpy_filter_genes" title="based on counts and numbers of cells expressed"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Scanpy FilterGenes</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=scanpy_filter_cells" title="based on counts and numbers of genes expressed"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Scanpy FilterCells</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=scanpy_compute_graph" title="to derive kNN graph"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Scanpy ComputeGraph</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=hca_matrix_downloader" title="retrieves expression matrices and metadata from the Human Cell Atlas."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Human Cell Atlas Matrix Downloader</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=_ensembl_gtf2gene_list" title="extracts a complete annotation table or subsets thereof from an Ensembl GTF using rtracklayer"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">GTF2GeneList</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ucsc_cell_browser" title="displays single-cell clusterized data in an interactive web application."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">UCSC Cell Browser</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=scanpy_parameter_iterator" title="produce an iteration over a defined parameter"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Scanpy ParameterIterator</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=scanpy_plot_trajectory" title="visualise cell trajectories"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Scanpy PlotTrajectory</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=scmap_index_cell" title="creates a cell index for a dataset to enable fast approximate nearest neighbour search"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Scmap index cells</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=retrieve_scxa" title="Retrieves expression matrixes and metadata from EBI Single Cell Expression Atlas (SCXA)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">EBI SCXA Data Retrieval</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ucsc_cell_browser" title="displays single-cell clusterized data in an interactive web application."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">UCSC Cell Browser</button></a>
 <h3 id="othertools">Other Tools</h3>
 <a href="https://usegalaxy.eu/root?tool_id=abstracts_by_pmids" title="by PMID IDs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Get PubMed abstracts</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=text_to_wordmatrix" title="by extracting most frequent words"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Text to wordmatrix</button></a>
@@ -3593,19 +3708,28 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=spring_mcc" title="plot generator"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SPRING MCC</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ffindex_dbkit_extract" title="entries"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">DBKit Extract</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=ffindex_dbkit_merge" title="two databases"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">DBKit Merge</button></a>
-<h3 id="biodiversitydataexploration">Biodiversity data exploration</h3>
-<a href="https://usegalaxy.eu/root?tool_id=tool_anonymization" title="without loss of the spatial relationships"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Spatial coordinates anonymization</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ecology_beta_diversity" title="Computes a measure of beta diversity, SCBD and representations"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Local Contributions to Beta Diversity (LCBD)</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ecology_homogeneity_normality" title="Checks the homogeneity of the variance and the normality of the distribution"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Homoscedasticity and normality</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ecology_link_between_var" title="Shows interaction, correlation, colinearity, produces a PCA and computes VIF for biodiversity abundance data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Variables exploration</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ecology_presence_abs_abund" title="Community abundance map, presence barplot and rarefaction curves"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Presence-absence and abundance</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ecology_stat_presence_abs" title="of a numeric variable"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Statistics on presence-absence</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=cb_div" title="indicators"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Diversity</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=obisindicators" title="from OBIS"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Ocean biodiversity indicators</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=pcdl_get_anndata" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">pcdl_get_anndata</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=pcdl_get_cell_attribute" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">pcdl_get_cell_attribute</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=pcdl_get_cell_attribute_list" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">pcdl_get_cell_attribute_list</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=pcdl_get_cell_df" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">pcdl_get_cell_df</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=pcdl_get_celltype_list" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">pcdl_get_celltype_list</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=pcdl_get_conc_attribute" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">pcdl_get_conc_attribute</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=pcdl_get_conc_df" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">pcdl_get_conc_df</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=pcdl_get_substrate_list" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">pcdl_get_substrate_list</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=pcdl_get_unit_dict" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">pcdl_get_unit_dict</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=pcdl_get_version" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">pcdl_get_version</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=pcdl_make_cell_vtk" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">pcdl_make_cell_vtk</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=pcdl_make_conc_vtk" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">pcdl_make_conc_vtk</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=pcdl_make_gif" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">pcdl_make_gif</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=pcdl_make_graph_gml" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">pcdl_make_graph_gml</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=pcdl_make_movie" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">pcdl_make_movie</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=pcdl_plot_contour" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">pcdl_plot_contour</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=pcdl_plot_scatter" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">pcdl_plot_scatter</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=pcdl_plot_timeseries" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">pcdl_plot_timeseries</button></a>
 <h3 id="sangersequencing">Sanger Sequencing</h3>
-<a href="https://usegalaxy.eu/root?tool_id=tracy_decompose" title="heterozygous mutations (and call variants)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">tracy Decompose</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=tracy_basecall" title="from Sanger chromatogram tracefile"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">tracy Basecall</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=tracy_align" title="chromatogram to a FASTA reference"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">tracy Align</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=tracy_decompose" title="heterozygous mutations (and call variants)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">tracy Decompose</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=tracy_assemble" title="genomic region from tiled, overlapping Sanger Chromatogram trace files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">tracy Assemble</button></a>
 <h3 id="extractfeatures">Extract Features</h3>
 <a href="https://usegalaxy.eu/root?tool_id=length_and_gc_content" title="from GTF and FASTA file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Gene length and GC content</button></a>
@@ -3613,21 +3737,10 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=orfipy" title="a versatile ORF finder"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ORFipy</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=b2btools_single_sequence" title="from their amino-acid sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">b2bTools: Biophysical predictors for single sequences</button></a>
 <h3 id="qiime2">QIIME 2</h3>
-<a href="https://usegalaxy.eu/root?tool_id=qiime2__sample_classifier__regress_samples" title="Train and test a cross-validated supervised learning regressor."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 sample-classifier regress-samples</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=qiime2__phylogeny__filter_tree" title="Remove features from tree based on metadata"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 phylogeny filter-tree</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=qiime2__metadata__shuffle_groups" title="Shuffle values in a categorical sample metadata column."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 metadata shuffle-groups</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=qiime2__longitudinal__pairwise_distances" title="Paired pairwise distance testing and boxplots"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 longitudinal pairwise-distances</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=qiime2__fragment_insertion__filter_features" title="Filter fragments in tree from table."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 fragment-insertion filter-features</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=qiime2__feature_table__merge_seqs" title="Combine collections of feature sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 feature-table merge-seqs</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=qiime2__feature_classifier__vsearch_global" title="VSEARCH global alignment search"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 feature-classifier vsearch-global</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=qiime2__feature_classifier__extract_reads" title="Extract reads from reference sequences."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 feature-classifier extract-reads</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=qiime2__diversity__alpha_correlation" title="Alpha diversity correlation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 diversity alpha-correlation</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=qiime2__dada2__denoise_single" title="Denoise and dereplicate single-end sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 dada2 denoise-single</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=qiime2__composition__add_pseudocount" title="Add pseudocount to table."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 composition add-pseudocount</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=qiime2__stats__facet_across" title="Facet across outer group"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 stats facet-across</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=qiime2__alignment__mafft" title="De novo multiple sequence alignment with MAFFT"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 alignment mafft</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=qiime2__alignment__mafft_add" title="Add sequences to multiple sequence alignment with MAFFT."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 alignment mafft-add</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=qiime2__alignment__mask" title="Positional conservation and gap filtering."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 alignment mask</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__composition__add_pseudocount" title="Add pseudocount to table."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 composition add-pseudocount</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=qiime2__composition__ancom" title="Apply ANCOM to identify features that differ in abundance."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 composition ancom</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=qiime2__composition__ancombc" title="Analysis of Composition of Microbiomes with Bias Correction"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 composition ancombc</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=qiime2__composition__tabulate" title="View tabular output from ANCOM-BC or ANCOM-BC2."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 composition tabulate</button></a>
@@ -3638,6 +3751,7 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=qiime2__dada2__denoise_ccs" title="Denoise and dereplicate single-end Pacbio CCS"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 dada2 denoise-ccs</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=qiime2__dada2__denoise_paired" title="Denoise and dereplicate paired-end sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 dada2 denoise-paired</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=qiime2__dada2__denoise_pyro" title="Denoise and dereplicate single-end pyrosequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 dada2 denoise-pyro</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__dada2__denoise_single" title="Denoise and dereplicate single-end sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 dada2 denoise-single</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=qiime2__deblur__denoise_other" title="Deblur sequences using a user-specified positive filter."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 deblur denoise-other</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=qiime2__deblur__visualize_stats" title="Visualize Deblur stats per sample."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 deblur visualize-stats</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=qiime2__demux__emp_paired" title="Demultiplex paired-end sequence data generated with the EMP protocol."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 demux emp-paired</button></a>
@@ -3648,6 +3762,7 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=qiime2__demux__summarize" title="Summarize counts per sample."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 demux summarize</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=qiime2__diversity__adonis" title="adonis PERMANOVA test for beta group significance"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 diversity adonis</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=qiime2__diversity__alpha" title="Alpha diversity"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 diversity alpha</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__diversity__alpha_correlation" title="Alpha diversity correlation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 diversity alpha-correlation</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=qiime2__diversity__alpha_group_significance" title="Alpha diversity comparisons"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 diversity alpha-group-significance</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=qiime2__diversity__alpha_phylogenetic" title="Alpha diversity (phylogenetic)"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 diversity alpha-phylogenetic</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=qiime2__diversity__alpha_rarefaction" title="Alpha rarefaction curves"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 diversity alpha-rarefaction</button></a>
@@ -3687,9 +3802,11 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=qiime2__feature_classifier__classify_consensus_vsearch" title="VSEARCH-based consensus taxonomy classifier"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 feature-classifier classify-consensus-vsearch</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=qiime2__feature_classifier__classify_hybrid_vsearch_sklearn" title="ALPHA Hybrid classifier: VSEARCH exact match + sklearn classifier"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 feature-classifier classify-hybrid-vsearch-sklearn</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=qiime2__feature_classifier__classify_sklearn" title="Pre-fitted sklearn-based taxonomy classifier"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 feature-classifier classify-sklearn</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__feature_classifier__extract_reads" title="Extract reads from reference sequences."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 feature-classifier extract-reads</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=qiime2__feature_classifier__find_consensus_annotation" title="Find consensus among multiple annotations."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 feature-classifier find-consensus-annotation</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=qiime2__feature_classifier__fit_classifier_naive_bayes" title="Train the naive_bayes classifier"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 feature-classifier fit-classifier-naive-bayes</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=qiime2__feature_classifier__fit_classifier_sklearn" title="Train an almost arbitrary scikit-learn classifier"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 feature-classifier fit-classifier-sklearn</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__feature_classifier__vsearch_global" title="VSEARCH global alignment search"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 feature-classifier vsearch-global</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=qiime2__feature_table__core_features" title="Identify core features in table"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 feature-table core-features</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=qiime2__feature_table__filter_features" title="Filter features from table"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 feature-table filter-features</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=qiime2__feature_table__filter_features_conditionally" title="Filter features from a table based on abundance and prevalence"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 feature-table filter-features-conditionally</button></a>
@@ -3698,6 +3815,7 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=qiime2__feature_table__group" title="Group samples or features by a metadata column"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 feature-table group</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=qiime2__feature_table__heatmap" title="Generate a heatmap representation of a feature table"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 feature-table heatmap</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=qiime2__feature_table__merge" title="Combine multiple tables"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 feature-table merge</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__feature_table__merge_seqs" title="Combine collections of feature sequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 feature-table merge-seqs</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=qiime2__feature_table__merge_taxa" title="Combine collections of feature taxonomies"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 feature-table merge-taxa</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=qiime2__feature_table__presence_absence" title="Convert to presence/absence"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 feature-table presence-absence</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=qiime2__feature_table__rarefy" title="Rarefy table"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 feature-table rarefy</button></a>
@@ -3708,6 +3826,7 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=qiime2__feature_table__tabulate_seqs" title="View sequence associated with each feature"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 feature-table tabulate-seqs</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=qiime2__feature_table__transpose" title="Transpose a feature table."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 feature-table transpose</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=qiime2__fragment_insertion__classify_otus_experimental" title="Experimental: Obtain taxonomic lineages, by finding closest OTU in reference phylogeny."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 fragment-insertion classify-otus-experimental</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__fragment_insertion__filter_features" title="Filter fragments in tree from table."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 fragment-insertion filter-features</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=qiime2__fragment_insertion__sepp" title="Insert fragment sequences using SEPP into reference phylogenies."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 fragment-insertion sepp</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=qiime2__gneiss__assign_ids" title="Assigns ids on internal nodes in the tree, and makes sure that they are consistent with the table columns."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 gneiss assign-ids</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=qiime2__gneiss__correlation_clustering" title="Hierarchical clustering using feature correlation."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 gneiss correlation-clustering</button></a>
@@ -3725,15 +3844,18 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=qiime2__longitudinal__maturity_index" title="Microbial maturity index prediction."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 longitudinal maturity-index</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=qiime2__longitudinal__nmit" title="Nonparametric microbial interdependence test"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 longitudinal nmit</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=qiime2__longitudinal__pairwise_differences" title="Paired difference testing and boxplots"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 longitudinal pairwise-differences</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__longitudinal__pairwise_distances" title="Paired pairwise distance testing and boxplots"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 longitudinal pairwise-distances</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=qiime2__longitudinal__plot_feature_volatility" title="Plot longitudinal feature volatility and importances"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 longitudinal plot-feature-volatility</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=qiime2__longitudinal__volatility" title="Generate interactive volatility plot"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 longitudinal volatility</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=qiime2__metadata__distance_matrix" title="Create a distance matrix from a numeric Metadata column"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 metadata distance-matrix</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__metadata__shuffle_groups" title="Shuffle values in a categorical sample metadata column."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 metadata shuffle-groups</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=qiime2__metadata__tabulate" title="Interactively explore Metadata in an HTML table"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 metadata tabulate</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=qiime2__phylogeny__align_to_tree_mafft_fasttree" title="Build a phylogenetic tree using fasttree and mafft alignment"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 phylogeny align-to-tree-mafft-fasttree</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=qiime2__phylogeny__align_to_tree_mafft_iqtree" title="Build a phylogenetic tree using iqtree and mafft alignment."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 phylogeny align-to-tree-mafft-iqtree</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=qiime2__phylogeny__align_to_tree_mafft_raxml" title="Build a phylogenetic tree using raxml and mafft alignment."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 phylogeny align-to-tree-mafft-raxml</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=qiime2__phylogeny__fasttree" title="Construct a phylogenetic tree with FastTree."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 phylogeny fasttree</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=qiime2__phylogeny__filter_table" title="Remove features from table if they're not present in tree."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 phylogeny filter-table</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__phylogeny__filter_tree" title="Remove features from tree based on metadata"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 phylogeny filter-tree</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=qiime2__phylogeny__iqtree" title="Construct a phylogenetic tree with IQ-TREE."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 phylogeny iqtree</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=qiime2__phylogeny__iqtree_ultrafast_bootstrap" title="Construct a phylogenetic tree with IQ-TREE with bootstrap supports."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 phylogeny iqtree-ultrafast-bootstrap</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=qiime2__phylogeny__midpoint_root" title="Midpoint root an unrooted phylogenetic tree."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 phylogeny midpoint-root</button></a>
@@ -3757,6 +3879,7 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=qiime2__sample_classifier__metatable" title="Convert (and merge) positive numeric metadata (in)to feature table."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 sample-classifier metatable</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=qiime2__sample_classifier__predict_classification" title="Use trained classifier to predict target values for new samples."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 sample-classifier predict-classification</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=qiime2__sample_classifier__predict_regression" title="Use trained regressor to predict target values for new samples."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 sample-classifier predict-regression</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__sample_classifier__regress_samples" title="Train and test a cross-validated supervised learning regressor."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 sample-classifier regress-samples</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=qiime2__sample_classifier__regress_samples_ncv" title="Nested cross-validated supervised learning regressor."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 sample-classifier regress-samples-ncv</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=qiime2__sample_classifier__scatterplot" title="Make 2D scatterplot and linear regression of regressor predictions."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 sample-classifier scatterplot</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=qiime2__sample_classifier__split_table" title="Split a feature table into training and testing sets."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 sample-classifier split-table</button></a>
@@ -3781,6 +3904,7 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=qiime2__stats__collate_stats" title="Combine and FDR correct multiple stats"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 stats collate-stats</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=qiime2__stats__wilcoxon_srt" title="Wilcoxon Signed Rank Test"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 stats wilcoxon-srt</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=qiime2__stats__plot_rainclouds" title="Raincloud plots"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 stats plot-rainclouds</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=qiime2__stats__facet_across" title="Facet across outer group"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 stats facet-across</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=qiime2__stats__facet_within" title="Facet within outer group"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 stats facet-within</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=qiime2__stats__prep_alpha_distribution" title="Alpha diversity to Dist1D"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 stats prep-alpha-distribution</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=qiime2__rescript__get_bv_brc_genome_features" title="Fetch genome features from BV-BRC."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">qiime2 rescript get-bv-brc-genome-features</button></a>
@@ -3798,74 +3922,66 @@ layout: default
 <a href="https://usegalaxy.eu/root?tool_id=find_diag_hits" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Find diagnostic hits</button></a>
 <h3 id="gatktools">GATK Tools</h3>
 <a href="https://usegalaxy.eu/root?tool_id=gatk_count_covariates" title="on BAM files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Count Covariates</button></a>
-<h3 id="xas(x-rayabsorptionspectroscopy)">XAS (X-ray Absorption Spectroscopy)</h3>
-<a href="https://usegalaxy.eu/root?tool_id=larch_select_paths" title="select FEFF paths for XAFS data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Larch Select Paths</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=larch_plot" title="plot Athena projects"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Larch Plot</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=larch_athena" title="generate Athena projects from XAFS data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Larch Athena</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=larch_artemis" title="generate Artemis projects from XAFS data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Larch Artemis</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=larch_feff" title="generate FEFF paths from XAFS data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Larch FEFF</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=larch_lcf" title="perform linear combination fit on XAS data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Larch LCF</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=larch_criteria_report" title="generate reports on Artemis fitting from XAFS data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Larch Criteria Report</button></a>
 <h3 id="built-inconverters">Built-in Converters</h3>
-<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_neostorezip_to_neostore" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert neostore.zip files to neostore</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_gff_to_bed_0" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert GFF to BED</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=CONVERTER_bcf_uncompressed_to_bcf" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert compressed and uncompressed BCF files</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_wig_to_bigwig" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert Wiggle to BigWig</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_interval_to_tabix_0" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert Interval to tabix</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_bam_to_coodinate_sorted_bam" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert BAM to coordinate-sorted BAM</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_archive_to_directory" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Unpack archive to directory</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=lped2pbedconvert" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert lped to plink pbed</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_bz2_to_uncompressed" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert compressed file to uncompressed.</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=pbed2ldindepconvert" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert plink pbed to ld reduced format</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_fastq_to_fqtoc0" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert FASTQ files to seek locations</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_uncompressed_to_gz" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert uncompressed file to compressed</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=CONVERTER_gz_to_uncompressed" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert compressed file to uncompressed.</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_bed_gff_or_vcf_to_bigwig_0" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert BED, GFF, or VCF to BigWig</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_bed_to_fli_0" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert BED to Feature Location Index</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_bam_to_bigwig_0" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert BAM to BigWig</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_interval_to_bed12_0" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert Genomic Intervals To Strict BED12</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_maf_to_fasta_0" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert MAF to Fasta</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=CONVERTER_mdconvert" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert XTC, DCD, and TRR</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=bigwigtowig" title="Convert bigWig to wig"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert BigWig to Wiggle</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_len_to_linecount" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert Len file to Linecount</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=ucsc_bigbedtobed" title="Convert bigBed to BED"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert from bigBed to ascii bed format.</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_fasta_to_len" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert FASTA to len file</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_fastq_to_fqtoc0" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert FASTQ files to seek locations</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_interval_to_tabix_0" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert Interval to tabix</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_biom" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert Biom datasets</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_cram_to_bam_0" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert CRAM to BAM</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_maf_to_interval_0" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert MAF to Genomic Intervals</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_SMILES_to_MOL" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert SMILES to MOL</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_wig_to_bigwig" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert Wiggle to BigWig</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_molecules" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">OpenBabel converter for molecular formats</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_interval_to_bedstrict_0" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert Genomic Intervals To Strict BED</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=CONVERTER_inchi_to_mol" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert InChI to MOL</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_Pdb_to_Gro_0" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert PDB to GRO</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=CONVERTER_interval_to_bgzip_0" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert Interval to BGZIP</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=CONVERTER_wiggle_to_interval_0" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert Wiggle to Interval</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_mol2_to_mol" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert MOL2 to MOL</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_Gro_to_Pdb_0" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert GRO to PDB</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_bz2_to_uncompressed" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert compressed file to uncompressed.</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_bam_to_qname_sorted_bam" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert BAM to queryname-sorted BAM</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_uncompressed_to_gz" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert uncompressed file to compressed</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_bed_to_gff_0" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert BED to GFF</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=CONVERTER_bedgraph_to_bigwig" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert BedGraph to BigWig</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_interval_to_bed_0" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert Genomic Intervals To BED</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_interval_to_bed6_0" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert Genomic Intervals To Strict BED6</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_maf_to_fasta_0" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert MAF to Fasta</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_bed_gff_or_vcf_to_bigwig_0" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert BED, GFF, or VCF to BigWig</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_maf_to_interval_0" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert MAF to Genomic Intervals</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_cram_to_bam_0" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert CRAM to BAM</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_bed_to_fli_0" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert BED to Feature Location Index</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=CONVERTER_vcf_bgzip_to_tabix_0" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert BGZ VCF to tabix</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=pbed2ldindepconvert" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert plink pbed to ld reduced format</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_sam_to_bigwig_0" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert SAM to BigWig</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_Bam_Bai_0" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert Bam to Bai</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=tabular_to_csv" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert tabular to CSV</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=CONVERTER_fasta_to_bowtie_color_index" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert FASTA to Bowtie color space Index</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_interval_to_bedstrict_0" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert Genomic Intervals To Strict BED</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_bam_to_bigwig_0" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert BAM to BigWig</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_gff_to_interval_index_0" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert GFF to Interval Index</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_interval_to_bigwig_0" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert Genomic Intervals To Coverage</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_ref_to_seq_taxomony" title="converts 2 or 3 column sequence taxonomy file to a 2 column mothur taxonomy_outline format"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert Ref taxonomy to Seq Taxonomy</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_fasta_to_fai" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert FASTA to fai file</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_smiles_to_smiles" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SMILES to SMILES</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=csv_to_tabular" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert CSV to tabular</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_parquet_to_csv" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert Parquet to csv</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_Gro_to_Pdb_0" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert GRO to PDB</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_fasta_to_bowtie_base_index" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert FASTA to Bowtie base space Index</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_interval_to_bed_0" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert Genomic Intervals To BED</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_picard_interval_list_to_bed6" title="converter"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert Picard Interval List to BED6</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_bam_to_qname_sorted_bam" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert BAM to queryname-sorted BAM</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=tabular_to_csv" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert tabular to CSV</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=CONVERTER_gff_to_fli_0" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert GFF to Feature Location Index</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_molecules" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">OpenBabel converter for molecular formats</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_cml_to_smiles" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert CML to SMILES</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=tabular_to_dbnsfp" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert tabular to dbnsfp</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_fasta_to_tabular" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert FASTA to Tabular</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_sam_to_bigwig_0" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert SAM to BigWig</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_SMILES_to_MOL" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert SMILES to MOL</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_biom" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert Biom datasets</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=lped2fpedconvert" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert lped to fped</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_interval_to_bed12_0" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert Genomic Intervals To Strict BED12</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=CONVERTER_sam_to_unsorted_bam" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert SAM to BAM without sorting</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=lped2pbedconvert" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert lped to plink pbed</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_parquet_to_csv" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert Parquet to csv</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_gff_to_bed_0" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert GFF to BED</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=pbed2lpedconvert" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert plink pbed to linkage lped</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_archive_to_directory" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Unpack archive to directory</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_smiles_to_smiles" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">SMILES to SMILES</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_bam_to_coodinate_sorted_bam" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert BAM to coordinate-sorted BAM</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_gff_to_interval_index_0" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert GFF to Interval Index</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_ref_to_seq_taxomony" title="converts 2 or 3 column sequence taxonomy file to a 2 column mothur taxonomy_outline format"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert Ref taxonomy to Seq Taxonomy</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_picard_interval_list_to_bed6" title="converter"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert Picard Interval List to BED6</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_neostorezip_to_neostore" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert neostore.zip files to neostore</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_interval_to_bed6_0" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert Genomic Intervals To Strict BED6</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_cml_to_smiles" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert CML to SMILES</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_len_to_linecount" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert Len file to Linecount</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=bigwigtowig" title="Convert bigWig to wig"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert BigWig to Wiggle</button></a>
 <a href="https://usegalaxy.eu/root?tool_id=CONVERTER_fasta_to_2bit" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert FASTA to 2bit</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_interval_to_bigwig_0" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert Genomic Intervals To Coverage</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_bed_to_gff_0" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert BED to GFF</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_fasta_to_bowtie_base_index" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert FASTA to Bowtie base space Index</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=csv_to_tabular" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert CSV to tabular</button></a>
-<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_fasta_to_fai" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert FASTA to fai file</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=tabular_to_dbnsfp" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert tabular to dbnsfp</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_fasta_to_len" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert FASTA to len file</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_Pdb_to_Gro_0" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert PDB to GRO</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=ucsc_bigbedtobed" title="Convert bigBed to BED"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert from bigBed to ascii bed format.</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_Bam_Bai_0" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert Bam to Bai</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_mol2_to_mol" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert MOL2 to MOL</button></a>
+<a href="https://usegalaxy.eu/root?tool_id=CONVERTER_fasta_to_tabular" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert FASTA to Tabular</button></a>