Reading Evolutionary Biology Group

BayesPhylogenies 1.1


BayesPhylogenies is a general package for inferring phylogenetic trees using Bayesian Markov Chain Monte Carlo (MCMC) or Metropolis-coupled Markov chain Monte Carlo (MCMCMC) methods. The program allows a range of models of gene sequence evolution, models for morphological traits, models for rooted trees, gamma and beta distributed rate-heterogeneity, and implements a 'mixture model' (Pagel and Meade, 2004) that allows the user to fit more than one model of sequence evolution, without partitioning the data.

A number of introductions to the use of MCMC methods and Bayesian inference as applied to phylogenies are available and so we merely describe the program and its commands here. If you use the program in your published work, we would be grateful if you would cite the Pagel and Meade (2004) paper.


BayesPhylogenies - Manual (PDF)

BayesPhylogenies - Windows
BayesPhylogenies - Mac (OS X )
BayesPhylogenies - Linux

BayesPhylogenies - Adaptive Evolution / Heterotachy model.

Back to Software