This repository contains a set of tools to perform various population genetic analyses on genomic data.
ABBA-BABA folder contains scripts to run the ABBA-BABA test of admixture.
calculate_AveragePerWindow.py calculates average values for non-overlapping sliding windows.
calculate_WindowAverage_perSNP.py calculates average values for a window centered on each SNP.
calculate_MedianPerWindow.py calculates median values per sliding window.
calculate_FixedHetero_PerWindow.py calculates fixed heterozygosity (exist in hybrids) with the sliding window approach.
calculate_Hetero_PerWindow.py calculates heterozygosity with the sliding window approach.
calculate_iHSproportion.py calculates fractions of SNPs with iHS values above 2.0 over genomic windows of specified size.
calculate_PositionMean.py calculates mean per position of a table with numbers.
calculate_Total-Hetero.py calculates total heterozygosity.
calculate_TotalMean.py calculates total mean of a table with numbers.
DAF.py calculates change in derived allele frequency (deltaDAF).
mutMatrix.py estimates a mutation matrix required for LDhelmet.
SFS.py reconstructs the site frequency spectrum for a given set of samples.
DISCLAIMER: USE THESE SCRIPTS AT YOUR OWN RISK. I MAKE NO WARRANTIES THAT THESE SCRIPTS ARE BUG-FREE, COMPLETE, AND UP-TO-DATE. I AM NOT LIABLE FOR ANY LOSSES IN CONNECTION WITH THE USE OF THESE SCRIPTS.