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.

Using PhyML

To run PhyML in MPI mode, you should setup the required PATH by command:

System 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.


Please cite:

“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.

Additional Information

Official documentation is available at PhyML Website