MrBayes

Description

mrbayes website  

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 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