# 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