PhyML

Description

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PhyML is a software that estimates maximum likelihood phylogenies from alignments of nucleotide or amino acid sequences. It provides a wide range of options that were designed to facilitate standard phylogenetic analyses. The main strengths 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. It also implements two methods to evaluate branch supports in a sound statistical framework (the non-parametric bootstrap and the approximate likelihood ratio test). PhyML was designed to process moderate to large data sets. In theory, alignments with up to 4,000 sequences 2,000,000 character-long can analyzed. In practice however, the amount of memory required to process a data set is proportional of the product of the number of sequences by their length. Hence, a large number of sequences can only be processed provided that they are short. Also, PhyML can handle long sequences provided that they are not numerous. With most standard personal computers, the “comfort zone” for PhyML generally lies around 3 to 500 sequences less than 2,000 character long.

Building: The source code for PhyML was obtained from the SVN repository. To build from source autoconf files had to be generated with autoreconf -f -i -s; autoconf Template:App Location

Available versions

• 3.0 (built on 03/05/12 from the source code)

Running the application using modules

To use phyml with the environment modules system at HPC the following commands are available:

Get module information for phyml:

$module spider phyml

Load the default application module:

$module load phyml

The modulefile for this software adds the directory with executable files to the shell execution PATH and sets the following environment variables:

• HPC_PHYML_DIR - directory where phyml is located.
• HPC_PHYML_BIN - executable directory.