PhyML
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.
License
GNU GPL 2
Usage
Upcoming modulesystem change alert!
Due to large number of applications and their versions it is not practical to keep them explicitly listed at our wiki pages. Therefore an upgrade of modulefiles is underway. A feature of this upgrade will be the existence of default module for every application. This default choice does not need version number and it will load some (usually latest) version.
You can test the new version now by adding a line
source /cvmfs/software.metacentrum.cz/modulefiles/5.1.0/loadmodules
to your script before loading a module. Then, you can list all versions of phyml and load default version of phyml as
module avail phyml/ # list available modules module load phyml # load (default) module
If you wish to keep up to the current system, it is still possible. Simply list all modules by
module avail phyml
and choose explicit version you want to 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
Documentation
https://github.com/stephaneguindon/phyml/blob/master/doc/phyml-manual.pdf