bModelTest: Bayesian site model selection for nucleotide data

Remco Bouckaert
doi: http://dx.doi.org/10.1101/020792

bModelTest allows for a Bayesian approach to inferring a site model for phylogenetic analysis. It is based on trans dimensional MCMC proposals that allow switching between substitution models, whether gamma rate heterogeneity is used and whether a proportion of the sites is invariant. The model can be used with the set of reversible models on nucleotides, but we also introduce other sets of substitution models, and show how to use these sets of models. With the method, the site model can be inferred during the MCMC analysis and does not need to be pre-determined, as is now often the case in practice, by likelihood based methods.