PyPop: Python for Population Genomics

SimRA (Simulation based on Random-graphs Algorithms) is a framework for simulating generic and complex evolutionary scenarios of multiple populations with subdivision and admixture. The algorithm g…

Espalier is a Python package for working with discordant phylogenetic trees using maximum agreement forests.

A Snakemake executor plugin for submitting jobs to Microsoft Azure Batch.

Approximate Bayesian Computation using Deep Learning (TensorFlow Keras backended) and Sequential Monte Carlo (aka Particle Filter)

The code coverage tool for Python

Sampling and inference of genealogies with recombination

Software package for BalLeRMix and scripts used in the study "Flexible mixture model approaches that accommodate footprint size variability for robust detection of balancing selection" (Cheng & DeG…

Code for the maximum likelihood solution to the epoch sampling skyline plot method of Parag, du Plessis and Pybus

Ancestral character reconstruction and visualisation for rooted phylogenetic trees

Cluster amino acid distributions for empirical distribution mixture models

orthology assignment using phylogenetic and network analyses

A machine learning algorithm for phylogenetic model selection

repository for code and releases of PIQMEE add-on for BEAST2

This repository contains the instructions and files to replicate the analyses performed in the `Gradient` paper of Ji et al.

Statistical analysis of gene family evolution using phylogenetic birth-death processes and WGD inference using rjMCMC

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

Program for estimating dN/dS in overlapping genes (OLGs)

Performing highly efficient genome scans for local adaptation with R package pcadapt v4

Repo for MS: "Relative model fit does not predict topological accuracy in single-gene protein phylogenetics"

CellCoal: coalescent simulation of single-cell NGS genotypes

PRANC is used to compute probabilities of ranked phylogenetic gene trees given a species tree under coalescent process.

Rapidly Evolving Long Exon Capture

Detecting context dependent mutation rates from NGS data