Tanthony@uab.edu: added category software

2012-04-04T14:08:56Z

added category software

← Older revision		Revision as of 14:08, 4 April 2012
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	qstat -u $USER		qstat -u $USER
	</pre>		</pre>

			[[Category:Software]]

Ppreddy@uab.edu: add submission and monitor info

2010-01-04T21:43:14Z

add submission and monitor info

← Older revision		Revision as of 21:43, 4 January 2010
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	echo "FINISH: $(date)"		echo "FINISH: $(date)"

			</pre>

			Then submit that script with
			<pre>
			qsub name-of-script-above
			</pre>

			Check on it with qstat.
			<pre>
			qstat -u $USER
	</pre>		</pre>

Ppreddy@uab.edu: initial:mrbayes

2010-01-04T21:10:12Z

initial:mrbayes

New page

[http://mrbayes.sourceforge.net/ 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

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

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

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

<pre>
!/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)"

</pre>

MrBayes - Revision history

Tanthony@uab.edu: added category software

Ppreddy@uab.edu: add submission and monitor info

Ppreddy@uab.edu: initial:mrbayes