Scripts used in the "The evolutionary history of the field vole species complex revealed by modern and ancient genomes"

This repository contains three Python scripts used for the analysis of field vole genomic data described in paper "The evolutionary history of the field vole species complex revealed by modern and ancient genomes". (DOI will be provided upon acceptance).All three scripts may be executed using Python software.2AllelesFilter_gzip.py - this scripts taks a gzipped haplofile produced by ANGSD's (https://www.popgen.dk/angsd) option --doHaplofile as an argument and filters out all the positions containing more than two alleles.CDeaminationFilter_gzip.py - this scripts taks a gzipped haplofile produced by ANGSD's (https://www.popgen.dk/angsd) option --doHaplofile as an argument and filters out all positions contains transitions (C->T).output_consensus_3fasta_v8.py - this script produces an ancestral state file used in divergence dating via TT-method (https://doi.org/10.1093/genetics/iyab008). It takes a FASTA formatted alignment of one contig from three spcecies and produces a ancestral state file as defined here: https://github.com/jammc313/TT-method