PhyloBayes
PhyloBayes is a Bayesian Monte Carlo Markov Chain (MCMC) sampler for phylogenetic reconstruction using protein alignments. Compared to other phylogenetic MCMC samplers, the main distinguishing feature of PhyloBayes is the underlying probabilistic model, CAT (Lartillot and Philippe, 2004). 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. NEW : an upgraded version of phylobayes (version 3) is now available. It allows for tree reconstruction and molecular dating analyses under a wide variety of substitution models. It is compatible with macOSX, Linux 32/64 bits and Windows.Download PhyloBayes CM (covarion mixture)
Coevol. Correlated evolution of substitution rates and phenotypes