library for nonlinear optimization, wrapping many algorithms for global and local, constrained or unconstrained, optimization

PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. Please report only **technical issues** on this repository (e.g., compiling, programs a…

Haplotype based scans for selection

Bayesian analysis of genomic sequence data under the multispecies coalescent model

Infer a tree sequence from genetic variation data.

Count-Min Sketch Implementation in C

GONE: Scripts, programs and an example data set

RAiSD: software to detect positive selection based on multiple signatures of a selective sweep and SNP vectors

G-PhoCS is a software package for inferring ancestral population sizes, population divergence times, and migration rates from individual genome sequences.

predicting DFE and alpha from polymorphism data

Inferring natural selection by comparative population genomic analysis across species

Within-species genome-wide dN/dS estimation from very many genomes

Software for detecting introgression using supervised machine learning

Ancestry_HMM-S is program designed to infer adaptive introgression from population genomic data

CellCoal: coalescent simulation of single-cell NGS genotypes

A statistical framework for reference-free inference of archaic local ancestry

HaploSweep is a method for detecting and categorizing soft and hard selective sweeps based on haplotype structure.

Population genetics tests and estimators for pooled NGS data

Check trees for compatibility with defined groupings in unrooted trees - "The incontestable clan test"

Source code of SweepNet

Rearrangement algorithms for genetic data