Bayesian MCMC phylogenetic inference

 BEAST is a cross-platform program for Bayesian MCMC analysis of molecular
 sequences. It is entirely orientated towards rooted, time-measured
 phylogenies inferred using strict or relaxed molecular clock models. It
 can be used as a method of reconstructing phylogenies but is also a
 framework for testing evolutionary hypotheses without conditioning on a
 single tree topology. BEAST uses MCMC to average over tree space, so that
 each tree is weighted proportional to its posterior probability. Included
 is a simple to use user-interface program for setting up standard
 analyses and a suit of programs for analysing the results.