RT Journal Article SR Electronic T1 bModelTest: Bayesian site model selection for nucleotide data JF bioRxiv FD Cold Spring Harbor Laboratory SP 020792 DO 10.1101/020792 A1 Remco Bouckaert YR 2015 UL http://biorxiv.org/content/early/2015/06/11/020792.abstract AB 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.