PhyML
Overview
PhyML is a phylogeny software with a good balance between accuracy and speed. An online version is also available for smaller jobs.
Availability
| Cluster | Module/Version |
|---|---|
| BOSE | Not Available |
| BGSC | phyml/3.3.20200621 |
Note: You can simply use "module load phyml" to activate the most recently installed version of this software.
Sample Slurm Script
submit.sh
#!/bin/bash
# -- SLURM SETTINGS -- #
# [..] other settings here [..]
# The following settings are for the overall request to Slurm
#SBATCH --ntasks-per-node=32 # How many CPU cores do you want to request
#SBATCH --nodes=1 # How many nodes do you want to request
# -- SCRIPT COMMANDS -- #
# Load the needed modules
module load PhyML # Load PhyML
Real Example
Has your research group used PhyML in a project? Contact the HPC Team and we'd be glad to feature your work.
Citation
Please include the following citation in your papers to support continued development of PhyML.
"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.