MrBayes

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Last Modified: 07/14 17:48

Description

MrBayes is a program for the Bayesian estimation of phylogeny. Bayesian inference of phylogeny is based upon a quantity called the posterior probability distribution of trees, which is the probability of a tree conditioned on the observations. The conditioning is accomplished using Bayes's theorem. The posterior probability distribution of trees is impossible to calculate analytically; instead, MrBayes uses a simulation technique called Markov chain Monte Carlo (or MCMC) to approximate the posterior probabilities of trees.

Version

• 3.1.2

Authorized Users

• circe account holders

Platforms

• circe cluster

Local Documentation

Modules

MrBayes requires the following module file and some prerequisites to run:

• apps/mrbayes/3.1.2
• Prerequisites: compilers/pgi/7.0-7.x86_64 openmpi/1.2.6-x86_64-pgi-7.0-7

To run MrBayes on the cluster, ensure that you use module initadd to make the changes persistent. See Modules for more information.

Running MrBayes Jobs on the Cluster

• The following job script will be adequate for running the current installation of MrBayes:

  #!/bin/bash
  #$ -N mrbayes_test
  #$ -cwd
  #$ -pe ompi* 4
  #$ -o output.$JOB_ID
  #$ -j y
  #$ -q amd64.q
  #$ -l h_rt=8:00:00
  
  # The exact path of the binary to be run must be listed when you use 'sge_mpirun'
  # This is because environment variables (such as PATH) are not sent to the executing shell
  sge_mpirun /opt/apps/mrbayes/mb < batchfile > outfile