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.Download PhyloBayes CM (covarion mixture)
Coevol: correlated evolution of substitution rates and phenotypes
Coevol is a Bayesian MCMC software for comparative analyses combining molecular data and continuous characters (e.g. ecological variables or life-history traits.)
The program takes as an input a multiple sequence alignment, a matrix of continuous characters, and a phylogenetic tree. It then jointly estimates:
- the divergence times
- the evolution of the continuous characters along the tree.
- the evolution of certain key parameters of the substitution process (e.g. the rate of substitution, the dN/dS ratio, or the GC content), again along the tree
- the correlations between continuous characters and substitution parameters (corrected for phylogenetic inertia)
The principles of the method are introduced in more details in Lartillot and Poujol, 2010, Molecular Biology and Evolution