Custom scripts used in the Genome Biology paper "Genomes reveal marked differences in the adaptive evolution between orangutan species".
Classes/ Contains Perl packages used in the scripts below.
vcftofasta.pl Perl script to generate individual FASTA sequences from VCF files.
print_snpdiff.pl Perl script to annotate SNPs and calculate allele frequency differences among populations.
generate_validbed.pl Perl script to generate a bed file of sufficiently covered genomic regions used to prepare input files for the momi2 analyses.