View source for PAML

[[Category:Software]][[Category:Bioinformatics]][[Category:Phylogenetics]]
{|<!--CONFIGURATION: REQUIRED-->
|{{#vardefine:app|paml}}
|{{#vardefine:url|http://abacus.gene.ucl.ac.uk/software/paml.html}}
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|{{#vardefine:conf|}}           <!--CONFIGURATION-->
|{{#vardefine:exe|1}}            <!--ADDITIONAL INFO-->
|{{#vardefine:pbs|}}            <!--PBS SCRIPTS-->
|{{#vardefine:policy|}}         <!--POLICY-->
|{{#vardefine:testing|}}       <!--PROFILING-->
|{{#vardefine:faq|}}             <!--FAQ-->
|{{#vardefine:citation|}}       <!--CITATION-->
|{{#vardefine:installation|}} <!--INSTALLATION-->
|}
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<!--Description-->
{{#if: {{#var: url}}|
{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}}

PAML is a package of programs for phylogenetic analyses of DNA or protein
sequences using maximum likelihood. It is maintained and distributed for
academic use free of charge by Ziheng Yang. PAML is not suitable for
building trees. It may be used to estimate parameters and test hypotheses to
study the evolutionary process when you have reconstructed trees using
other programs such as PAUP*, PHYLIP, MOLPHY, PhyML, RaxML, etc.
<!--Modules-->
==Required Modules==
===Serial===
* {{#var:app}}
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===Parallel (OpenMP)===
* intel
* {{#var:app}}
===Parallel (MPI)===
* intel
* openmpi
* {{#var:app}}
-->
==System Variables==
* HPC_{{#uppercase:{{#var:app}}}}_DIR - installation directory
* HPC_{{#uppercase:{{#var:app}}}}_BIN - executable directory
* HPC_{{#uppercase:{{#var:app}}}}_CTL - sample .ctl files directory
* HPC_{{#uppercase:{{#var:app}}}}_DOC - documentation directory
* HPC_{{#uppercase:{{#var:app}}}}_EX - examples directory
<!--Configuration-->
{{#if: {{#var: conf}}|==Configuration==
See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.
|}}
<!--Run-->
{{#if: {{#var: exe}}|==Additional Information==

Most of the binaries in this package require appropriate .ctl files. Copy sample .ctl files from the $HPC_PAML_CTL directory to your working directory and modify them before running the programs. There are sample datasets in $HPC_PAML_EX.
|}}
<!--PBS scripts-->
{{#if: {{#var: pbs}}|==PBS Script Examples==
See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.
|}}
<!--Policy-->
{{#if: {{#var: policy}}|==Usage Policy==
WRITE USAGE POLICY HERE (Licensing, usage, access).
|}}
<!--Performance-->
{{#if: {{#var: testing}}|==Performance==
WRITE_PERFORMANCE_TESTING_RESULTS_HERE
|}}
<!--Faq-->
{{#if: {{#var: faq}}|==FAQ==
*'''Q:''' **'''A:'''|}}
<!--Citation-->
{{#if: {{#var: citation}}|==Citation==
If you publish research that uses {{#var:app}} you have to cite it as follows:
WRITE_CITATION_HERE
|}}
<!--Installation-->
{{#if: {{#var: installation}}|==Installation==
See the [[{{PAGENAME}}_Install]] page for {{#var: app}} installation notes.|}}
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