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Software: 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.

Available Versions

Unspecified: 3.2.7

MrBayes is available both in a serial version ('mb') and in a parallel version ('mb-mpi') that uses MPI instructions to distribute computations across several processors or processor cores. The serial version does not support multi-threading, which means that you will not be able to utilize more than one core on a multi-core machine for a single MrBayes analysis. If you want to utilize all cores,you need to run the MPI version of MrBayes.

Note: 'mb-mpi' in this version of the container does not run across multiple nodes (only within a node). This is a bug in the container (upstream).

For more information, please check its website: https://biocontainers.pro/tools/mrbayes and its home page: http://mrbayes.net.

Commands

  • mb
  • mb-mpi
  • mpirun
  • mpiexec

Module

You can load the modules by:

module load biocontainers
module load mrbayes

Example job

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run MrBayes on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name 
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=mrbayes
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers mrbayes