View source for PhyML

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[[Category:Software]][[Category:Biology]][[Category:Phylogenetics]]
{|<!--Main settings - REQUIRED-->
|{{#vardefine:app|phyml}}
|{{#vardefine:url|http://code.google.com/p/phyml/}}
|{{#vardefine:exe|}} <!--Present manual instructions for running the software -->
|{{#vardefine:conf|}} <!--Enable config wiki page link - {{#vardefine:conf|1}} = ON/conf|}} = OFF-->
|{{#vardefine:pbs|}} <!--Enable PBS script wiki page link-->
|{{#vardefine:policy|}} <!--Enable policy section -->
|{{#vardefine:testing|}} <!--Enable performance testing/profiling section -->
|{{#vardefine:faq|}} <!--Enable FAQ section -->
|{{#vardefine:citation|}} <!--Enable Reference/Citation section -->
|}
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<!--Description-->
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{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}}

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 [http://code.google.com/p/phyml/source/checkout SVN repository]. To build from source autoconf files had to be generated with <code>autoreconf -f -i -s; autoconf</code>
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==Environment Modules==
Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
==System Variables==
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
* HPC_PHYML_BIN - executable directory.
{{#if: {{#var: exe}}|==How To Run==
WRITE INSTRUCTIONS ON RUNNING THE ACTUAL BINARY|}}
{{#if: {{#var: conf}}|==Configuration==
See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.|}}
{{#if: {{#var: pbs}}|==PBS Script Examples==
See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}}
{{#if: {{#var: policy}}|==Usage Policy==
WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used)|}}
{{#if: {{#var: testing}}|==Performance==
WRITE PERFORMANCE TESTING RESULTS HERE|}}
{{#if: {{#var: faq}}|==FAQ==
*'''Q:''' **'''A:'''|}}
{{#if: {{#var: citation}}|==Citation==
If you publish research that uses {{{app}}} you have to cite it as follows:
WRITE CITATION HERE
|}}