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MrBayes

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[[Category:Software]]

Latest revision as of 09:08, 4 April 2012

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.

The program takes as input a character matrix in a NEXUS file format. The output is several files with the parameters that were sampled by the MCMC algorithm.

[edit] Steps to run MrBayes

MrBayes works with Intel and GNU openmpi libraries. Once you login to Cheaha, set up your environment to work against a particular flavor of openmpi. For example, to work with Intel openmpi, you would do the following before using MrBayes

export compiler="intel"
module load mrbayes/mrbayes-${compiler}

Replace "intel" to "gnu", if using gnu openmpi

Here's a sample script to run MrBayes on an SGE scheduler

!/bin/bash
############################################################
#                Setting up the environment
#$ -S /bin/bash
#$ -cwd
#
#$ -N j_mrbayes_parallel
#$ -pe openmpi 8
#$ -l h_rt=15:00:00,s_rt=14:55:00
#$ -j y
#
#$ -M YOUR_EMAIL_ADDRESS
#$ -m eas
#
# Load the appropriate module files
export compiler="intel"
module load mrbayes/mrbayes-${compiler}
#$ -V

echo "START:  $(date)"
mpirun -np $NSLOTS mb-mpi mrbayes_batch.input

echo "FINISH: $(date)"

Then submit that script with

qsub name-of-script-above

Check on it with qstat.

qstat -u $USER