PhyML

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Description

PhyML - Phylogenetic estimation using (Maximum) Likelihood. hyML is a software that estimates maximum likelihood phylogenies from alignments of nucleotide or amino acid sequences. The main strength of PhyML lies in the large number of substitution models coupled to various options to search the space of phylogenetic tree topologies, going from very fast and efficient methods to slower but generally more accurate approaches.


Availability

Program is available in version 3.0 and 3.1

Use

Initialize enviroment for

  • one processor run
module add phyml-3.0
phyml
  • multi processor run
module add phyml-3.0-mpi
mpiexec phyml

our you can use version with Intel compiler

module add phyml-3.0-impi
mpirun phyml-mpi -i InputFile
  • version 3.1
module add phyml-3.1
phyml -h

License

GNU GPL 2.

Documentation

Documentation is available on WWW server or http://www.atgc-montpellier.fr/download/papers/phyml_manual_2012.pdf

Program administrator

meta@cesnet.cz

Homepage

URL: http://code.google.com/p/phyml/ URL: http://www.atgc-montpellier.fr/phyml/