PHYML

Category(ies): Bioinformatics

Version: updated at 03/07/2008

Author / Distributor:
Stéphane Guindon, Olivier Gascuel LIRMM, Montpellier, France

PHYML is a software implementing a new method for building phylogenies from DNA and protein sequences using maximum likelihood.
Please refer to PHYML for more details.

altix: Not available on altix

pcluster: Not available on pcluster

rcluster,IOB: running program | Documentation | Installation | System

Running Program: also refer to submit jobs to queues at rcluster,IOB

Please refer to PHYML Commands for detail commands

Type 13 parameters for DNA sequences :

phyml sequences file data type sequence format nb data sets nb bootstrapped data sets substitution model ts/tv ratio prop. invariable sites nb categories gamma parameter starting tree optimise topology optimise branch lengths and rate parameters

Type 12 parameters for amino-acids sequences :

phyml sequences file data type sequence format nb data sets nb bootstrapped data sets substitution model prop. invariable sites nb categories gamma parameter starting tree optimise topology optimise branch lengths and rate parameters

bsub -q queueName phyml parameters... -o filename.out

Documentation: Online document available at PHYML website

Installation: binary code downloaded from PHYML AMD-64 website.

System(s): Unix