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Revision as of 11:20, 18 July 2016 by Theath (talk | contribs)

Course materials by Tracy Heath and Michael Landis on substitution models and phylogenetic reconstruction in RevBayes

Background Reading

  • Höhna et al. 2016. RevBayes: Bayesian phylogenetic inference using graphical models and an interactive model-specification language. Systematic Biology, 65:726-736. (PDF)
  • Höhna et al. 2014. Probabilistic graphical model representation in phylogenetics. Systematic Biology 63:753–771. (PDF)


  • Introduction to RevBayes slides
  • RevBayes script for demo: lnorm.Rev

Phylogenetic Inference using RevBayes: Substitution Models for Unconstrained Trees


Software downloads, tutorials, documentation, and other resources can be found on the RevBayes web page:

RevBayes source code can be found on GitHub:


The detailed lab practical document can be found here: tutorial PDF

Help files

Online Help Files

  • Search for RevBayes commands in the upper right corner.
  • Filter by command type by (un-)checking boxes.

Data & Analysis Files

On the MBL Cluster

On the course cluster create a directory to run your analysis:

mkdir RB_tutorial
cd RB_tutorial

Download the data directory containing the data file:


Un-zip the downloaded file (this will create a directory containing the file "primates_cytb.nex"


Execute RevBayes:


Additional Software