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JOURNAL ARTICLE
RESEARCH SUPPORT, NON-U.S. GOV'T
RESEARCH SUPPORT, U.S. GOV'T, NON-P.H.S.
Phylogenetic Inference Using RevBayes.
Current Protocols in Bioinformatics 2017 May 3
Bayesian phylogenetic inference aims to estimate the evolutionary relationships among different lineages (species, populations, gene families, viral strains, etc.) in a model-based statistical framework that uses the likelihood function for parameter estimates. In recent years, evolutionary models for Bayesian analysis have grown in number and complexity. RevBayes uses a probabilistic-graphical model framework and an interactive scripting language for model specification to accommodate and exploit model diversity and complexity within a single software package. In this unit we describe how to specify standard phylogenetic models and perform Bayesian phylogenetic analyses in RevBayes. The protocols focus on the basic analysis of inferring a phylogeny from single and multiple loci, describe a hypothesis-testing approach, and point to advanced topics. Thus, this unit is a starting point to illustrate the power and potential of Bayesian inference under complex phylogenetic models in RevBayes. © 2017 by John Wiley & Sons, Inc.
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