How to use phylobayes

Software	Version	Cluster
phylobayes	1.8c	Dardel

Phylobayes is a Bayesian Monte Carlo Markov Chain (MCMC) sample for phylogenetic reconstruction. Compared to other phylogenetic MCMC samplers, the main distinguishing feature of PhyloBayes is the underlying probabilistic model, CAT. CAT is an infinite mixture model accounting for site-specific amino-acid or nucleotide preferences. It is well suited to phylogenomic studies using large multigene alignment.

After adding the module PhyloBayes can be run:

module load PDC
module load Phylobayes-MPI

with the following example command:

salloc -N 2 -t 15:00:00 aprun -n 64 pb_mpi -f -d convo9849.ali -cat -gtr -dgam 4 -dc catgtrconvo

Example data for this command can be found in::

/pdc/vol/phylobayes/1.5a/data

Disclaimer

PDC takes no responsibility for the correctness of results produced with the binaries. Always evaluate the binaries against known results for the systems and properties you are investigating before using the binaries for production jobs.