Hi, Dear Dr. Faircloth,
I am trying to find UCEs within parasites genomes. However, didn't found the get_conserved_sequence.py script described in the workflow of UCE identification http://baddna.github.io/seqcap/workflows.html.
Am I looking at a wrong place? I searched your other repositories under https://github.com/faircloth-lab and didn't find this script and flag_cons_duplicates.py. I saw a script at faircloth-lab/phyluce/bin/attic/remove_duplicate_hits_from_fasta_using_lastz.py. Is that an updated version? It needs a lastz input, which should be generated first, I guess by alignment/easy_lastz.py?
Thanks for your time!
Lijing
UNM CETI