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.

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.

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