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Phylobayes

Phylobayes is a Bayesian sampler and will perform phylogenetic reconstruction using either nucleotide, protein, or codon sequence alignments.

Phylobayes is available as a module on Apocrita.

Versions

Phylobayes and the MPI enabled version have been installed on Apocrita (using OpenMPI). We recommend using the MPI version where possible, which is accessible with the phylobayes-mpi module (see the parallel job example for further usage).

For single node, non-MPI jobs, use the phylobayes module as documented below.

MPI binary names are suffixed with _mpi, for example pb_mpi.

Usage

To run the latest installed version of Phylobayes, simply load the phylobayes module:

$ module load phylobayes
$ pb

pb [options] <chainname>
    creates a new chain, sampling from the posterior distribution, conditional
    on specified data

data options:
    -d <filename>      : file containing an alignment in phylip or nexus format;
                         dna, rna or amino acids

tree:
    -t <treefile>       : starts from specified tree
    -T <treefile>       : chain run under fixed, specified tree
    -r <outgroup>       : re-root the tree (useful under clock models)

For full usage documentation, run pb -help.

Specifying the end point of the chain

If you do not specify the number of points after which the chain should stop (-x flag), the chain will run indefinitely and cause the job to fail by exceeding the requested runtime.

Example jobs

Serial job

Here is an example job running on 1 core and 5GB memory of memory executing the sample data provided in the test_data sub-directory.

#!/bin/sh
#$ -cwd
#$ -pe smp 1
#$ -l h_rt=4:0:0
#$ -l h_vmem=2G

module load phylobayes

export TEST_DATA_PATH=/share/apps/centos7/phylobayes/test_data

pb -d ${TEST_DATA_PATH}/animalfung6317912.puz \
   -t ${TEST_DATA_PATH}/animalfungi.tre \
   -x 5 20 \
   animalfungi

Parallel job

Here is an example job running across two nxv nodes, executing the sample data provided in the test_data sub-directory.

#!/bin/sh
#$ -cwd
#$ -pe parallel 64
#$ -l infiniband=nxv
#$ -l h_rt=4:0:0

module load phylobayes-mpi

export TEST_DATA_PATH=/share/apps/centos7/phylobayes-mpi/test_data

mpirun -np ${NSLOTS} pb_mpi \
   -d ${TEST_DATA_PATH}/animalfung6317912.puz \
   -t ${TEST_DATA_PATH}/animalfungi.tre \
   -x 5 20 \
   animalfungi

References