A Bayesian Monte Carlo Markov Chain (MCMC) sampler for phylogenetic reconstruction using protein alignments. Compared to other phylogenetic MCMC samplers (e.g. MrBayes), the main distinguishing feature of PhyloBayes is the underlying probabilistic model, CAT. CAT is a mixture model especially devised to account for site-specific features of protein evolution. It is particularly well suited for large multigene alignments, such as those used in phylogenomics.