MrBayes is a program for Bayesian inference of phylogeny using Markov Chain Monte Carlo methods. MrBayes has a console interface and uses a modified NEXUS format for data and batch files. It handles a wide range of probabilistic models for the evolution of nucleotide and amino acid sequences, restriction sites, and standard binary data.
To run this software interactively in a Linux environment run the commands:
module load mrbayes
For documentation, refer to the MrBayes homepage.
MrBayes is also installed on Cascade. This version has been compiled to use GPU and MPI processing.
This is a sample PBS script for running MrBayes on Cascade:

#!/bin/bash -l

#PBS -l walltime=01:00:00,pmem=2500mb,nodes=1:ppn=4:gpus=4:cascade

#PBS -m abe

#PBS -q cascade


module load mrbayes

cd /path/to/your/working/directory

mpirun -hostfile $PBS_NODEFILE -np 4 mb <mb_parms.txt > primates_out.txt

Where mb_parms is a MrBayes batch command file. Please read the MrBayes documentation for valid MrBayes commands.
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