Phylogenetic Inference Using RevBayes

Sebastian Höhna1, Michael J. Landis2, Tracy A. Heath3

1 Department of Statistics, University of California, Berkeley, 2 Department of Ecology & Evolutionary Biology, Yale University, New Haven, Connecticut, 3 Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, Iowa
Publication Name:  Current Protocols in Bioinformatics
Unit Number:  Unit 6.16
DOI:  10.1002/cpbi.22
Online Posting Date:  May, 2017
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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.

Keywords: Bayesian phylogenetics; Markov chain Monte Carlo; posterior probabilities; probabilistic graphical models; substitution model

     
 
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Table of Contents

  • Introduction
  • Basic Protocol 1: Estimating Phylogeny (Topology and Branch Lengths)
  • Basic Protocol 2: Partitioned Data Analysis
  • Basic Protocol 3: Model Comparison Using Bayes Factors
  • Guidelines for Understanding Results
  • Commentary
  • Literature Cited
  • Figures
  • Tables
     
 
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Materials

Basic Protocol 1: Estimating Phylogeny (Topology and Branch Lengths)

  Necessary Resources
  • All of the necessary resources for this tutorial are described above in protocol 1. All data files and analysis scripts are available for download from the RevBayes Web site http://revbayes.com/tutorials. html.
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Figures

Videos

Literature Cited

Literature Cited
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