Difference between revisions of "Amphora2"

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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
* HPC_{{#uppercase:{{#var:app}}}}_BIN - executable directory
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* HPC_{{uc:{{#var:app}}}}_BIN - executable directory
* HPC_{{#uppercase:{{#var:app}}}}_DOC - documentation directory
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* HPC_{{uc:{{#var:app}}}}_DOC - documentation directory
* HPC_{{#uppercase:{{#var:app}}}}_EXE - test data directory
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* HPC_{{uc:{{#var:app}}}}_EXE - test data directory
* HPC_{{#uppercase:{{#var:app}}}}_TAX- taxonomy data directory
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* HPC_{{uc:{{#var:app}}}}_TAX- taxonomy data directory
* HPC_{{#uppercase:{{#var:app}}}}_TREE - tree data directory
+
* HPC_{{uc:{{#var:app}}}}_TREE - tree data directory
  
 
<!--Configuration-->
 
<!--Configuration-->

Latest revision as of 17:35, 10 June 2022

Description

amphora2 website  

An Automated Phylogenomic Inference Pipeline for Bacterial and Archaeal Sequences.

AMPHORA2 is free software: you may redistribute it and/or modify its under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or any later version.

Environment Modules

Run module spider amphora2 to find out what environment modules are available for this application.

System Variables

  • HPC_AMPHORA2_DIR - installation directory
  • HPC_AMPHORA2_BIN - executable directory
  • HPC_AMPHORA2_DOC - documentation directory
  • HPC_AMPHORA2_EXE - test data directory
  • HPC_AMPHORA2_TAX- taxonomy data directory
  • HPC_AMPHORA2_TREE - tree data directory




Citation

If you publish research that uses amphora2 you have to cite it as follows:

Wu M, Scott AJ. Phylogenomic analysis of bacterial and archaeal sequences with AMPHORA2. Bioinformatics 2012; 28(7):1033-1034