Wang, X., ... Heller, R. (2025). Population structure and domestication history of the Javan banteng.
Scripts to evaluate assembly.
A pipeline for mapping and post-mapping filtering using PALEOMIX BAM pipeline.
Script to assess post-mortem damage in historical samples using mapDamage2;
A pipeline designed to remove problematic samples prior to downstream analyses;
Script to perform a second and more sensitive analysis of relatedness within each sampling location using NgsRelate.
A pipeline designed to avoid biases from low-quality mapping sites.
A pipeline designed to call genotype likelihood for output as BEAGLE.
A pipeline designed to call genotypes;
Scripts to imputate and phase genotypes.
Script to infer principal component analysis (PCA) using HaploNet;
Script to estimate admixture proportions for each individual using NGSadmix;
Script to use evalAdmix.
Script to calculate genome-wide heterozygosity;
Script to infer Pairwise global Fst between each pair of populations;
Script to infer runs of homozygosity (ROH);
Script to calculate genome-wide heterozygosity without ROH.
Script to infer the population tree assuming different numbers of admixture events using TreeMix;
Script to infer the ancient admixture events, we calculated D statistics (ABBA-BABA) using the ANGSD;
Script to infer the f3-outgroup using the R package ADMIXTOOLS2.
Script to infer effective population size changes using PSMC;
Script to estimate domestication event between wild (Banteng-WildBorn) and domesticated (Bali-Bali) using Fastsimcoal2;
Script to estimate Confidence interval using Fastsimcoal2;
Script to perform simulations and calculate their Fst and pi during revision;
All 14 demographic model design for estimating domestication event by Fastsimcoal2.
Script to perform sliding window Fst, nucleotide diversity and Tajima’s D;
Script to infer linkage disequilibrium by ngsLD;
Script to infer XP-EHH (Sabhrina).
Scripts to infer genetic load.