MrBayes

Description

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.

In addition to the official MrBayes 3.2.1 distribution, a modified version that uses the Gamma-Dirichlet and Inverse Gamma-Dirichlet priors for branch lengths (Rannala et al. in press; Zhang et al. 2012). This also includes the two exponential priors on internal and external branch lengths described by Yang & Rannala (2005) and Yang (2007). Please see Ziheng Yang's site for more information and citations. The modified version is only installed for openmpi and is called mb_Dirichlet. To run this version, simply replace mb with mb_Dirichlet in the examples below.

Required Modules

modules documentation

Serial

mrbayes

Parallel (OpenMP)

intel
mrbayes

Parallel (OpenMPI)

intel
openmpi
mrbayes

System Variables

HPC_{{#uppercase:mrbayes}}_DIR - installation directory

PBS Script Examples

For MPI jobs: Remember that the total number of cores cannot be greater than the total number of chains MrBayes is using. For example, if you have 2 runs, each with 4 chains, the maximum number of cores to request is 2*4=8 cores. As long as the number of cores is under 12, it is best to keep nodes=1 (nodes = physical machines) as that will keep all communication within a single node. If you need more than 12 cores, you will probably want to add :infiniband to the request. (e.g. nodes=4:ppn=8:infiniband).

{{#fileAnchor: mrbayes.MPI.pbs}} Download raw source of the [{{#fileLink: mrbayes.MPI.pbs}} mrbayes.MPI.pbs]

#!/bin/bash
#
#PBS -N mrbayes
#PBS -M <your e-mail>
#PBS -m abe
#PBS -o mb.$PBS_JOBID.out
#PBS -e mb.$PBS_JOBID.err
#PBS -l nodes=1:ppn=8
#PBS -l pmem=500mb
#PBS -l walltime=01:00:00
#
# Change to the directory from which the job was submitted
#
cd $PBS_O_WORKDIR
#
# Use modules to configure your environment for mrbayes
#
module load intel
module load openmpi
module load mrbayes
#
# Run MrBayes using the command line from documentation.
#
mpiexec mb my_nexus.nex

Script for serial (single core) MrBayes job: {{#fileAnchor: mrbayes.serial.pbs}} Download raw source of the [{{#fileLink: mrbayes.serial.pbs}} mrbayes.serial.pbs]

#!/bin/bash
#
#PBS -N mrbayes
#PBS -M <your e-mail>
#PBS -m abe
#PBS -o mb.$PBS_JOBID.out
#PBS -e mb.$PBS_JOBID.err
#PBS -l nodes=1:ppn=1
#PBS -l pmem=500mb
#PBS -l walltime=01:00:00
#
# Change to the directory from which the job was submitted
#
cd $PBS_O_WORKDIR
#
# Use modules to configure your environment for mrbayes
#
module load mrbayes
#
# launch the executable
#
mb my_nexus.nex