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MrBayes

Category of SoftwareBioinformatics
What is MrBayesMrBayes is a program which performs Bayesian inference of phylogeny.
How to useA simple 4-slot MrBayes submit script is as follows; it uses the primates.nex sample script which you can copy from the MrBayes installation directory.

Sample Script

First copy input files to your directory as described below.

Script
#!/bin/sh
#$ -S /bin/sh
#$ -pe orte 4
#$ -cwd
#$ -l h_rt=12:00:00
#$ -l h_vmem=2G
module load mrbayes
# copy this file before beginning
#cp /opt/sw/mrbayes-3.2.1/examples/primates.nex .
#
 mpirun mb <<EOF
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
sump burnin=250
sumt burnin=250
quit
EOF

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