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 |
|---|---|
| HPC2021 | module load phyml |
then execute (or add this line to SLURM 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
Citation
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