RevBayes activities

Table of contents

 

Literature

Getting started

RevBayes provides an interactive environment for statistical computation in phylogenetics. It is primarily intended for modeling, simulation, and Bayesian inference in evolutionary biology, particularly phylogenetics. However, the environment is quite general and can be useful in any field dealing with complex stochastic models.

RevBayes uses its own language, Rev, which is similar to the language used in R. Like the R language, Rev is designed to support interactive analysis. Important differences include the support in Rev for object-oriented programing and for stepwise construction of complex models.

This summary page provides links to the four RevBayes activities that are part of the Workshop schedule. In addition to the below tutorial files, you may find these two introductory tutorials helpful:

  1. A general overview of RevBayes and the Rev language: RB_Getting_Started.pdf
  2. Basic Rev commands: RB_Basics_Tutorial.pdf

We recommend that all RevBayes activities are run using the RevBayes installation on the Amazon Machine Image (AMI). Since a graphical user interface is not needed for these activities, please connect to the AMI using ssh or PuTTY. Since we had to make a last-minute update to the revbase executable, you will need to re-download a newly compiled version from the evomics webpage to your AMI. To do so, please run the following commands after you have logged in to your AMI with either ssh or PuTTY:

wget http://evomics.org/wp-content/uploads/2015/02/rb

chmod +x rb

sudo mv rb /usr/local/bin

You may have to confirm and type your password in order to execute the last of the three commands. Next, prepare a directory for the RevBayes activity with

mkdir ~/wme_jan2015/activities/RevBayes

mkdir ~/wme_jan2015/activities/RevBayes/activity1

And while we’re at it, you might as well type

mkdir ~/wme_jan2015/activities/RevBayes/activity2

mkdir ~/wme_jan2015/activities/RevBayes/activity3

mkdir ~/wme_jan2015/activities/RevBayes/activity4

Then move into the directory of the first activity with

cd ~/wme_jan2015/activities/RevBayes/activity1

 

Activity 1 (Feb 2): RevBayes Introduction — Continuous-Time Markov Chains

This tutorial gives a general introduction to RevBayes and demonstrates how to set up and perform analyses using common nucleotide substitution models. You will need the following files for this exercise:

  1. Tutorial: RB_CTMC_Tutorial.pdf

  2. Example script: JukesCantor.Rev

    Download it from the course website to your AMI with

    wget http://evomics.org/wp-content/uploads/2015/02/RB1/JukesCantor.Rev

  3. Input file: primates_cytb.nex

    Download it from the course website to your AMI with

    wget http://evomics.org/wp-content/uploads/2015/02/RB1/primates_cytb.nex

 

Activity 2 (Feb 2): Bayes Factors and Model Selection

This tutorial demonstrates some general principles of Bayesian model comparison, which is based on estimating the marginal likelihood of competing models and then comparing their relative fit to the data using Bayes factors.

  1. Tutorial: RB_BayesFactor_Tutorial.pdf
  2. Example script: marginalLikelihood_JukesCantor.Rev Download it from the course website to your AMI with

    wget http://evomics.org/wp-content/uploads/2015/02/RB2/marginalLikelihood_JukesCantor.Rev

  3. Input file: primates_16s.nex Download it from the course website to your AMI with

    wget http://evomics.org/wp-content/uploads/2015/02/RB2/primates_16s.nex

  4. Input file: primates_cox2.nex Download it from the course website to your AMI with

    wget http://evomics.org/wp-content/uploads/2015/02/RB2/primates_cox2.nex

  5. Input file: primates_cytb.nex Download it from the course website to your AMI with

    wget http://evomics.org/wp-content/uploads/2015/02/RB2/primates_cytb.nex

 

Activity 3 (Feb 5): Biogeography and Large State Space Models

This tutorial demonstrates biogeographic analyses using RevBayes.

Once again we had to make a last-minute update to the revbase executable, so you will again need to re-download a newly compiled version from the evomics webpage to your AMI. So, please run the following commands after you have logged in to your AMI with either ssh or PuTTY:

wget http://evomics.org/wp-content/uploads/2015/05/rb

chmod +x rb

sudo mv rb /usr/local/bin

You may have to confirm and type your password in order to execute these commands. Next, move into the directory for the RevBayes activity with

cd ~/wme_jan2015/activities/RevBayes/activity3

Then, please download the following input files to your machine (the tutorial pdf) or to the AMI (all other files, using wget):

  1. Tutorial: RB_Biogeography_Tutorial.pdf

  2. Input files: biogeographyinputfiles.zip

    Download it from the course website to your AMI with

    wget http://evomicsorg.wpengine.netdna-cdn.com/wp-content/uploads/2015/02/biogeographyinputfiles.zip

    and unzip using the command

    unzip biogeographyinputfiles.zip

    additionally: earth25.still.atlas.txt

  3. Example script: Biogeography_DEC_equal.Rev

    Download it from the course website to your AMI with

    wget http://evomics.org/wp-content/uploads/2015/02/RB3/Biogeography_DEC_equal.Rev

  4. Example script: Biogeography_DEC_manyArea.Rev

    Download it from the course website to your AMI with

    wget http://evomics.org/wp-content/uploads/2015/02/RB3/Biogeography_DEC_manyArea.Rev

  5. Example output and output parsing script: RevBayes_Biogeography_ManyAreas_output

    Download it from the course website to your AMI with

    wget http://evomicsorg.wpengine.netdna-cdn.com/wp-content/uploads/2015/02/RevBayes_Biogeography_ManyAreas_output.zip

Useful reading on Bayesian Analaysis of Biogeography: http://sysbio.oxfordjournals.org/content/62/6/789
 

Activity 4 (Feb 5): Phylogenetic Comparative Methods

The subject of this tutorial is the analysis of trait evolution at the macroevolutionary scale.

  1. Tutorial: RB_PhyloComparative_Tutorial.pdf
  2. Example script: primatesMass_REML.Rev Download it from the course website to your AMI with

    wget http://evomics.org/wp-content/uploads/2015/02/RB4/primatesMass_REML.Rev

  3. Input file: primates_cytb.nex Download it from the course website to your AMI with

    wget http://evomics.org/wp-content/uploads/2015/02/RB4/primates_cytb.nex

  4. Input file: primates_lhtlog.nex Download it from the course website to your AMI with

    wget http://evomics.org/wp-content/uploads/2015/02/RB4/primates_lhtlog.nex

  5. Input file: primates.tree Download it from the course website to your AMI with

    wget http://evomics.org/wp-content/uploads/2015/02/RB4/primates.tree