View source for Applications/MrBayes

__TOC__
=== Application Details ===
* 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.
* Versions: 3.2.6
* Module names: mrbayes/gcc/3.2.6
* License: Available to all; GNU General Public License version 2.0 (GPLv2)

== Usage Examples ==
=== Executables ===
{| class="wikitable" style="background-color:#f5f5dc;"
! Executable
! Description
|-
| mb
| Single core and/or interactive
|-
| mb-mpi
| OpenMPI parallel version
|}
=== Interactive ===
<pre style="background-color: #000000; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
[username@c170 ~]$ mb


                            MrBayes v3.2.6 x64

                      (Bayesian Analysis of Phylogeny)

              Distributed under the GNU General Public License


               Type "help" or "help <command>" for information
                     on the commands that are available.

                   Type "about" for authorship and general
                       information about the program.


MrBayes >
</pre>
=== Batch Submission ===
A better approach is to submit a MrBayes task as a parallel batch submission to run across multiple nodes, an example of which is:

<pre style="background-color: #E5E4E2; color: black; font-family: monospace, sans-serif;">
#!/bin/bash
#SBATCH -J MrBTest          # Job name, you can change it to whatever you want
#SBATCH -N 4                # Number of nodes to run across
#SBATCH -n 100              # Number of cores to run across
#SBATCH -o %N-%j.log        # Standard output will be written here
#SBATCH -e %N-%j.err        # Standard error will be written here
#SBATCH -p compute          # Slurm partition, where you want the job to be queued

module add openmpi/gcc/1.10.5 mrbayes/gcc/3.2.6

mpirun -mca pml cm -mca mtl psm2 mb-mpi input_nex_file.nex
</pre> 
 
The options for mpirun are required to make use of the Omni-Path interconnect.

This submission script can be found at /path/to/sample/script

<pre style="background-color:#000000; color: white; font-family: monospace, sans-serif;">
[username@login01 ~]$ sbatch MRBayes.job
Submitted batch job 289555
</pre>

== Further Information ==
* [http://mrbayes.sourceforge.net/ MrBayes website]
* [[Main Page#General_Support|Wiki: General Support]]
* [[Programming/OpenMPI|Wiki: OpenMPI]]
* [[Main Page|Wiki: Home]]