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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.


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.


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

    -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.

#$ -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 \

Parallel job

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

#$ -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 \