Actively Developed Software

BayesAss Version 3 (BA3)

Software for inferring proportions of recent migrants among populations using multilocus genotype data. Publications with Commentary

Current Release (Version 3.04) Download.

BA3 Manual Download.

Bayesian Phylogenetics and Phylogeography (BPP)

Software for inferring Bayesian posterior probabilities of phylogenetic trees and/or species delimitations and related parameters under a multi-species coalescent process. Publications with Commentary

BPP version 4 now under development at

Current stable release of command line program BPP (Version 3.4) Download.

Minimalist BPP

Web application to generate control and map files for the BPP program. Default priors for theta and tau are specified using the uploaded sequence data. The average pairwise difference among sequences within populations specifies the prior mean of theta and the maximum pairwise difference specifies the prior mean of tau. Access the application here: bpps

Static Software (Supported but not developed)

Disequilibrium Mapping and Likelihood Estimation (DMLE+)

Software for disequilibrium gene mapping and allele age estimation. Publications with Commentary

DMLE+ website

Inference of Recombination Rates and Hotspots (InferRho)

Software for estimating recombination rates, gene conversion rates and recombination hotspot positions using Bayesian inference and the full likelihood for genome-wide SNP data. Publications with Commentary

Source code for InferRho version 1.0 Download

oncoSpectrum Version 1.2

ML program for estimating mutation rates using cancer mutation databases. Publication with Commentary

Source code for oncoSpectrum version 1.2 Download

Bayesian Phylogenetic Analysis with Site-specific Rates (BYPASSR)

Software for inferring the posterior distribution of site-specific rates using a gamma distribution prior without discretization and for inferring branch lengths on trees with DNA degradation (ancient DNA samples). Publications with Commentary

Source code for BYPASSR available at Ligia Mateiu’s website

Ancient Software (Unsupported and not developed)

ML Estimation of Bacterial Allele Frequencies (BACTFREQ)

Software for maximum likelihood estimation of bacterial allele frequencies (replaces BFREQ program). Program written by Eric Anderson. Publications with Commentary

Source code for BACTFREQ Download