What is PhyML?
PhyML stands for Phylogenetic Maximum Likelihood. It is a phylogeny software based on the maximum-likelihood principle to estimate maximum likelihood phylogenies from alignments of nucleotide or amino acid sequences.
To run PhyML in MPI mode, you should setup the required PATH by command:
|HPC2015||module load phyml|
then execute (or add this line to PBS job command file):
mpirun -np [NPROCS] phyml sequences_file data_type format data_sets bootstrap_sets model [kappa] invar nb_categ alpha tree opt_topology opt_lengths
Sample data sets and PBS job command file are available at /share1/phyml/sample.
“New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0.”
Guindon S., Dufayard J.F., Lefort V., Anisimova M., Hordijk W., Gascuel O.
Systematic Biology, 59(3):307-21, 2010.
Official documentation is available at PhyML Website