MrBayes
Overview
MrBayes is a program for the Bayesian inference of phylogeny, which uses
prior beliefs about a paramater.
Setup
To use MrBayes, it is necessary to set the environment by running a
special command sequence once per login session. You may optionally
place these commands in your .cshrc (C Shell users) or .bash_profile (Bourne Shell users) to avoid having to manually run these commands on login.
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For csh and tcsh:
source /usr/local/setup/mrbayes.setup.csh
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For sh and bash:
. /usr/local/setup/mrbayes.setup.sh
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Usage
MrBayes can be invoked using the command mrbayes followed by an input
file.
Examples
The following is an example PBS script to run a MrBayes job on LION-XE
for a maximum of 10 hours. The input file is called foo.nex and is a
standard NEXUS file of aligned nucleotide or amino acid sequences.
This file is in the directory /home/foo/mrbayes.
#PBS -l nodes=1:ppn=1
#PBS -l walltime=10:00:00
#PBS -j oe
# setup the MrBayes environment
. /usr/local/setup/mrbayes.setup.sh
# change the current working directory to the directory
# that contains the input files.
cd /home/foo/mrbayes
# run MrBayes
mrbayes foo.nex
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Further information on PBS scripts and submitting jobs on the LION-XE
and LION-XL clusters can be found in the User Guides section of the HPC
website.
Documentation
Information on MrBayes can be found on LION-XE in the directory
/usr/global/mrbayes. The manual is in acrobat format and can be viewed
by issuing the command:
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acroread /usr/global/mrbayes/manual.pdf
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Please send questions or suggestions about this web page to beatnic@aset.psu.edu
ASET | ITS | Penn State
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