MrBayes

MrBayes is a program for the Bayesian estimation of phylogeny. At MCSR both serial and parallel version of MrBayes 3 is available on Sequoia.

Serial MrBayes

Serial MrBayes 3 is installed in Sequoia at /usr/local/apps/mrbayes/mrbayes-3.1.2 and the executable is at /usr/local/apps/mrbayes/mrbayes-3.1.2/mb.

You should use PBS to submit your MrBayes jobs. Here is a sample script to create a job that runs on a node and accepts inputfile.nex as input file and creates a output file called outputfile.
#PBS -S /bin/csh
#PBS -l software=mrbayes
#PBS -l nodes=1:ppn=1
#PBS -q MCSR-Test
cd $HOME/Your Working Dir
/usr/local/apps/mrbayes/mrbayes-3.1.2/mb << EOF > outputfile
execute inputfile.nex;
quit;
EOF


Parallel MrBayes

Parallel MrBayes 3 is installed in Sequoia at /usr/local/apps/mrbayes_p/mrbayes-3.1.2 and the executable is at /usr/local/apps/mrbayes_p/mrbayes-3.1.2/mb.

You should use PBS to submit your MrBayes jobs. Here is a sample script that runs on 4 node and accepts inputfile.nex as input file and creates a output file called outputfile.
#PBS -S /bin/csh
#PBS -l software=mrbayes
#PBS -l ncpus=4
#PBS -q MCSR-Test
cd $HOME/Your Working Dir
mpiexec -n 4 /usr/local/apps/mrbayes_p/mrbayes-3.1.2/mb inputfile.nex > outputfile