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Note: Some of the information on this page is for our legacy systems only. The page is scheduled for an update to make it applicable to Graham.
MrBAYES
Description: Bayesian estimation of phylogeny
SHARCNET Package information: see MrBAYES software page in web portal
Full list of SHARCNET supported software



Introduction

MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. MrBayes uses Markov chain Monte Carlo (MCMC) methods to estimate the posterior distribution of model parameters.

Version Selection

Kraken and Requin have the newer version:

module load mrbayes/3.2.2

In Angel, Brown, Goblin, Hound, Iqaluk, Monk, Orca, Redfin, Saw, Wobbie, only 3.1.2 version can be used.

module load mrbayes/3.1.2

Job Submission

The MrBayes job can be submitted in a batch file which indicates both the Nexus file and your settings. The batch file(e.g batch.txt) should be located in the same dictionary with the Nexus file.

sqsub -r 1h -o my.out mb batch.txt

Example Job

A MrBayes batch file is done by adding a MRBAYES block to a Nexus file, either the same file containing the DATA block or a separate Nexus file. The MrBayes block simply contains the commands as you would have given them from the command line, with the difference that each command line is ended with a semi-colon. For instance, a MrBayes block that performs three single-run analyses of the dataset primates.nex and stores each result in a separate file is given below:

begin mrbayes;
   set autoclose=yes nowarn=yes;
   execute primates.nex;
   lset nst=6 rates=gamma;
   mcmc nruns=1 ngen=10000 samplefreq=10 file=primates.nex1;
   mcmc file=primates.nex2;
   mcmc file=primates.nex3;
end;

The "batch.txt" file containing this text above will be used as an Nexus file.

General Notes

If you need a newer version of MrBayes, please submit a ticket or send email to help@sharcnet.ca

References

o MrBayes Homepage
http://mrbayes.csit.fsu.edu/