Custom code used in "Morphometric, behavioural, and genomic evidence for a new orang-utan species".

Classes/ Contains Perl packages used in the scripts below.

filter_vcf.pl Perl script used to filter VCF files by max site-wise sequencing coverage (SI Section 2.1).

vcftofasta.pl Perl script used to generate individual FASTA sequences from VCF files (SI section 2.3).

getMatrixFromVCF.pl Perl script used to generate genotype matrices from a VCF files for PCA (SI Section 8.2).

genomescan_withinsamplingareas.pl Perl script used to calculate summary statistics within sampling areas (Fig. 2B).

genomescan_withinpops.pl Perl script used to calculate summary statistics within populations (SI Section 8.4).

generateGPhocs.pl Perl script used to generate input files for the G-PhoCS analysis (SI 11.1).

genomescan_3groups.pl Perl script used to calculate summary statistics within and among the three species (SI Section 12).

VCF_toFasta.jar Java program used to generate individual FASTA sequences from Y-chromosomal genotypes (SI section 7.2).

postABC-0.50/ C++ program used to generate summary statistics of simulated data for the ABC analysis (SI Section 10).