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ICHEC Software

Information about software packages installed on the ICHEC systems.

PhyloBayes

Versions Installed

Fionn: 3.3f / 1.5a (MPI)

Description

PhyloBayes is a Bayesian Monte Carlo Markov Chain (MCMC) sampler for phylogenetic reconstruction using protein alignments. Compared to other phylogenetic MCMC samplers (e.g. MrBayes), the main distinguishing feature of PhyloBayes is the underlying probabilistic model, CAT. It is particularly well suited for large multigene alignments, such as those used in phylogenomics.

Benchmarks

N/A.

Additional Notes

To use Phylobayes load the relevant environment module:

module load bio phylobayes/intel/3.3f

module load bio phylobayes/intel_mpi/1.5a

Further information can be obtained from http://megasun.bch.umontreal.ca/People/lartillot/www/index.htm.

Phylobayes 3.3f is serial. Multiple instances of blat can be run using task farming, see https://www.ichec.ie/support/documentation/task_farming.

Phylobayes 1.5a is a fully parallelised version of phylobayes, below is an example of a sumbmission script.

Job Submission Example

#!/bin/bash
#PBS -l nodes=2:ppn=24
#PBS -l walltime=00:10:00
#PBS -N MyJobName
#PBS -A MyProjectName
#PBS -j oe

module load libs intel-runtime/2013-sp1 module load bio phylobayes-mpi/intel/1.5a
cd $PBS_O_WORKDIR
module list

echo "Running test"
mpiexec pb_mpi -d datafile -cat -gtr chainname

exit 0

How to cite PhyloBayes:

Nicolas Lartillot, Thomas Lepage and Samuel Blanquart, PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating, (2009) Phylogenetics 25, 2286-2288.

Nicolas Lartillot and Hervé Philippe, A Bayesian Mixture Model for Across-Site Heterogeneities in the Amino-Acid Replacement Process, (2004) Mol. Biol. Evolution, 21,1095-1109.

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