Phylogenetic Inference Using RevBayes. Issue 1 (2nd May 2017)

• Record Type: Journal Article
• Authors: Höhna, Sebastian; Landis, Michael J.; Heath, Tracy A.
• Editors: Bateman, Alex; Pearson, William R.; Stein, Lincoln D.; Stormo, Gary D.; Yates, John R.
• Is Part Of: Current protocols in bioinformatics. Volume 57:Issue 1(2017)
• Page Start: 6.16.1
• Page End: 6.16.34
• Publication Date: 2017-05-02
• Subjects: Bayesian phylogenetics -- Markov chain Monte Carlo -- posterior probabilities -- probabilistic graphical models -- substitution model; Bioinformatics -- Laboratory manuals; Nucleotide sequence -- Laboratory manuals; Amino acid sequence -- Laboratory manuals; Base Sequence; Amino Acid Sequence; Computational Biology -- methods; Databases, Genetic; Proteins -- analysis; Sequence Analysis -- methods; Sequence Homology; Amino acid sequence; Bioinformatics; Nucleotide sequence; Laboratory Manuals; Laboratory manuals; 570.285
• DOI: 10.1002/cpbi.22
• Languages: English
• ISSNs: 1934-3396

Abstract

Abstract: 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.