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.
Usage¶
To run the default installed version of Phylobayes, simply load the
phylobayesmpi module:
$ module load phylobayesmpi
$ pb_mpi
mpirun -np <np> pb_mpi -d <datafile> [options] <chainname>
creates a new chain, sampling from the posterior distribution,
conditional on specified data
For full usage documentation, run pb_mpi without any flags.
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 job¶
Parallel job¶
Here is an example job running on 96 cores across 2 ddy nodes with MPI:
#!/bin/bash
#$ -cwd
#$ -j y
#$ -pe parallel 96
#$ -l infiniband=ddy-i
#$ -l h_rt=240:0:0
module load phylobayesmpi
mpirun -np ${NSLOTS} pb_mpi \
-d test.puz \
-t test.tre \
-x 5 20 \
test