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ICHEC Software

Information about software packages installed on the ICHEC systems.

MrBayes

Versions Installed

Fionn: 3.2.3-rev855 / 3.2.2

Description

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.

License

MrBayes is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version. The program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details

Benchmarks

N/A.

Additional Notes

To use MrBayes load the relevant environment module:

module load bio mrbayes/intel/r855
module load bio mrbayes/intel/3.2.2

Further information can be obtained from MrBayes: Home and the MrBayes Wiki.

Mrbayes is enabled for parallel execution. An example of how to submit a job to the queue is below.

Job Submission Example

#!/bin/bash
#PBS -l nodes=1:ppn=24
#PBS -l walltime=00:10:00
#PBS -N MyJobName
#PBS -A MyProjectName
#PBS -j oe

module load bio mrbayes/intel/r855
cd $PBS_O_WORKDIR
module list

echo "Running test"
mpiexec -n 2 mb << eof
execute primates.nex
eof

exit 0

This job can be submitted using the command

qsub scriptname.pbs

Where scriptname.pbs is the filename of the sample PBS script

How to cite MrBayes:

Run the citation command from the interface. The main references are below.

Huelsenbeck J. P., Ronquist F., Nielsen R. and Bollback J.P. (2001)
Bayesian inference of phylogeny and its impact on evolutionary biology.
Science 294: 2310-2314.

Ronquist F. and Huelsenbeck J.P. (2003)
MRBAYES 3: Bayesian phylogenetic inference under mixed models.
Bioinformatics 19: 1572-1574.

Ronquist, F. et al. 2012. MRBAYES 3.2: Efficient Bayesian phylogenetic
inference and model selection across a large model space. Systematic
Biology 61 (3): 539-542.

Altekar, G., S. Dwarkadas, J. P. Huelsenbeck, and F. Ronquist. (2004).
Parallel Metropolis-coupled Markov chain Monte Carlo for Bayesian
phylogenetic inference. Bioinformatics 20:407-415.

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