MrBayes

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.

Program features include:

  • A common command-line interface across Macintosh, Windows, and UNIX operating systems;
  • Extensive help available from the command line;
  • Analysis of nucleotide, amino acid, restriction site, and morphological data;
  • Mixing of data types, such as molecular and morphological characters, in a single analysis;
  • Easy linking and unlinking of parameters across data partitions;
  • An abundance of evolutionary models, including 4 X 4, doublet, and codon models for nucleotide data and many of the standard rate matrices for amino acid data;
  • Estimation of positively selected sites in a fully hierarchical Bayesian framework;
  • Full integration of the BEST algorithms for the multi-species coalescent.
  • Support for complex combinations of positive, negative, and backbone constraints on topologies;
  • Model jumping across the GTR model space and across fixed rate matrices for amino acid data;
  • Monitoring of convergence during the analysis, and access to a wide range of convergence diagnostics tools after the analysis has finished;
  • Rich summaries of posterior samples of branch and node parameters printed to majority rule consensus trees in FigTree format;
  • Implementation of the stepping-stone method for accurate estimation of model likelihoods for Bayesian model choice using Bayes factors;
  • The ability to spread jobs over a cluster of computers using MPI (for Macintosh (OS X) and UNIX environments only);
  • Support for the BEAGLE library, resulting in dramatic speedups for codon and amino acid models on compatible hardware (NVIDIA graphics cards);
  • Checkpointing across all models, allowing the user to seemlessly extend a previous analysis or recover from a system crash;

Utilisation

  • Chargement du module
$ module load bio/mrbayes
  • Exécution séquentiel
mrbayes_seq.sge
#!/bin/bash -l
 
#$ -l h_rt=2:00:0
#$ -o $JOB_NAME.o$JOB_ID
#$ -e $JOB_NAME.e$JOB_ID
#$ -N job_mrbayes_seq
#$ -V
 
module load bio/mrbayes
 
mb monscript
  • Exécution parallèle

Utiliser la version bio/mrbayes/mpi/3.2.6

mrbayes_mpi.sge
#!/bin/bash
#$ -q parallel.q
#$ -V
#$ -N job_mrbayes_mpi
#$ -pe mpi 32
#$ -o $JOB_NAME.$JOB_ID.out
 
module load bio/mrbayes/mpi/3.2.6
 
mpirun -np $NSLOTS mb monscript