P4 is a Python package for maximum likelihood and Bayesian analysis of molecular sequences.
MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. MrBayes uses Markov chain Monte Carlo (MCMC) methods to estimate the posterior distribution of model parameters.
JAGS is Just Another Gibbs Sampler. It is a program for analysis of
BUCKy is a free program to combine molecular data from multiple loci.