Difference between revisions of "PHAST"

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(Created page with "Category:SoftwareCategory:Biology[[Category:Phylogenetics] {|<!--CONFIGURATION: REQUIRED--> |{{#vardefine:app|phast}} |{{#vardefine:url|http://compgen.cshl.edu/phast/}...")
 
 
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[[Category:Software]][[Category:Biology]][[Category:Phylogenetics]
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[[Category:Software]][[Category:Biology]][[Category:Phylogenetics]]
 
{|<!--CONFIGURATION: REQUIRED-->
 
{|<!--CONFIGURATION: REQUIRED-->
 
|{{#vardefine:app|phast}}
 
|{{#vardefine:app|phast}}
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<!--Modules-->
 
<!--Modules-->
==Required Modules==
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==Environment Modules==
 
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Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
===Serial===
 
* {{#var:app}}
 
<!--
 
===Parallel (OpenMP)===
 
* intel
 
* {{#var:app}}
 
===Parallel (MPI)===
 
* intel
 
* openmpi
 
* {{#var:app}}
 
-->
 
 
==System Variables==
 
==System Variables==
* HPC_{{#uppercase:{{#var:app}}}}_DIR - installation directory
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* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
 
<!--Configuration-->
 
<!--Configuration-->
 
{{#if: {{#var: conf}}|==Configuration==
 
{{#if: {{#var: conf}}|==Configuration==

Latest revision as of 17:17, 10 June 2022

Description

phast website  

PHAST is a freely available software package for comparative and evolutionary genomics. It consists of about half a dozen major programs, plus more than a dozen utilities for manipulating sequence alignments, phylogenetic trees, and genomic annotations (see left panel). For the most part, PHAST focuses on two kinds of applications: the identification of novel functional elements, including protein-coding exons and evolutionarily conserved sequences; and statistical phylogenetic modeling, including estimation of model parameters, detection of signatures of selection, and reconstruction of ancestral sequences. It consists of over 60,000 lines of C code.

Environment Modules

Run module spider phast to find out what environment modules are available for this application.

System Variables

  • HPC_PHAST_DIR - installation directory