KimTree
Inferring population histories using genome-wide allele frequency data
Overview

The software package KimTree implements a hierarchical Bayesian model to estimate divergence times (in a diffusion time scale) in a population tree, from large single nucleotide polymorphism (SNP) data. The joint analysis of autosomal and X-linked polymorphisms further allows KimTree to infer the effective sex ratios or ESR (defined as the female proportion of the effective population), along each branch. The manual provides information about how to format the data file, how to specify the user-defined parameters, and how to interpret the results.

Citations

Gautier M and Vitalis R (2013) Inferring population histories using genome-wide allele frequency data. Molecular Biology and Evolution 30: 654-668 https://doi.org/10.1093/molbev/mss257

Clemente F, Gautier M and Vitalis R (2018) Inferring sex-specific demographic history from SNP data. PLoS Genetics 14(1): e1007191 https://doi.org/10.1371/journal.pgen.1007191