MrBayes

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.

Availability & Restrictions

MrBayes is available without restriction to all OSC users.

The following versions of MrBayes are available:

Version Glenn Oakley
3.1.2 X  
3.2.1   X

Usage

Set-up

To load the MrBayes software on the Glenn system, use the following commands:

module load biosoftw
module load mrbayes

On the Oakley system, use the following command:

module load mrbayes

Using MrBayes

Once mrbayes module is loaded, the commands are available for your use. The command for serial version is

mb

Parallel Mrbayes can only be used via batch system. The command is

mb-parallel

Batch Usage

Below is a sample batch script for running serial mrbayes job. It asks for 1 processor and 30 minutes of walltime.

#PBS -l walltime=30:00
#PBS -l nodes=1:ppn=1
#PBS -N mb
#PBS -j oe
set -x
date
cd $PBS_O_WORKDIR
cp ./primates.nex $TMPDIR
cp ./primates.nxs $TMPDIR
cd $TMPDIR
module load mrbayes-3.1.2
/usr/bin/time mb ./primates.nxs > mb.log
cp * $PBS_O_WORKDIR
date

Below is a sample batch script for running a parallel job on Oakley. It asks for 2 nodes, 24 processors and 30 minutes of walltime.

#PBS -l walltime=30:00
#PBS -l nodes=2:ppn=12
#PBS -N mb-parallel
#PBS -j oe
set -x
date
cd $PBS_O_WORKDIR
pbsdcp ./primates.nex $TMPDIR
pbsdcp ./primates.nxs $TMPDIR
cd $TMPDIR
module load mrbayes
/usr/bin/time mpiexec mb-parallel ./primates.nxs > mb-paralllel.log
pbsdcp -g '*' $PBS_O_WORKDIR
date

Further Reading

See Also

  • Paup
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