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.
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 |
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
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
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