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Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
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Phylogenetic Inference Using RevBayes.

Sebastian Höhna1,2, Michael J Landis3, Tracy A Heath4

  • 1Department of Integrative Biology, University of California, Berkeley, California.

Current Protocols in Bioinformatics
|May 3, 2017
PubMed
Summary
This summary is machine-generated.

Bayesian phylogenetic inference uses statistical models to estimate evolutionary relationships. RevBayes software facilitates complex phylogenetic analyses with its flexible model specification and scripting language.

Keywords:
Bayesian phylogeneticsMarkov chain Monte Carloposterior probabilitiesprobabilistic graphical modelssubstitution model

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Area of Science:

  • Evolutionary biology
  • Computational biology
  • Statistical modeling

Background:

  • Bayesian phylogenetic inference estimates evolutionary relationships using model-based statistical frameworks and likelihood functions.
  • The number and complexity of evolutionary models for Bayesian analysis have increased significantly.
  • Existing software can struggle to accommodate diverse and complex model specifications.

Purpose of the Study:

  • To describe the specification of standard phylogenetic models and the execution of Bayesian phylogenetic analyses in RevBayes.
  • To provide a starting point for utilizing RevBayes for complex phylogenetic modeling.
  • To illustrate the power and potential of Bayesian inference with complex models.

Main Methods:

  • Utilizing RevBayes, a software package employing a probabilistic-graphical model framework.
  • Employing an interactive scripting language for flexible model specification.
  • Focusing on protocols for inferring phylogenies from single and multiple loci and hypothesis testing.

Main Results:

  • Demonstration of how to specify standard phylogenetic models within RevBayes.
  • Successful execution of Bayesian phylogenetic analyses using RevBayes.
  • Illustration of hypothesis-testing approaches within the software.

Conclusions:

  • RevBayes offers a unified software package to accommodate model diversity and complexity in Bayesian phylogenetic inference.
  • The described protocols serve as an introduction to the capabilities of RevBayes for advanced phylogenetic analyses.
  • Bayesian inference in RevBayes provides a powerful approach for complex evolutionary modeling.