Difference between revisions of "Amphora2"

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|{{#vardefine:testing|}}      <!--PROFILING-->
 
|{{#vardefine:testing|}}      <!--PROFILING-->
 
|{{#vardefine:faq|}}            <!--FAQ-->
 
|{{#vardefine:faq|}}            <!--FAQ-->
|{{#vardefine:citation|}}      <!--CITATION-->
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|{{#vardefine:citation|1}}      <!--CITATION-->
 
|{{#vardefine:installation|}} <!--INSTALLATION-->
 
|{{#vardefine:installation|}} <!--INSTALLATION-->
 
|}
 
|}
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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
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* HPC_{{uc:{{#var:app}}}}_TREE - tree data directory
  
 
<!--Configuration-->
 
<!--Configuration-->
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{{#if: {{#var: testing}}|==Performance==
 
{{#if: {{#var: testing}}|==Performance==
  
Wu M, Scott AJ. Phylogenomic analysis of bacterial and archaeal sequences with AMPHORA2. Bioinformatics 2012; 28(7):1033-1034
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|}}
 
|}}
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If you publish research that uses {{#var:app}} you have to cite it as follows:
 
If you publish research that uses {{#var:app}} you have to cite it as follows:
  
WRITE_CITATION_HERE
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[https://www.ncbi.nlm.nih.gov/pubmed/22332237 Wu M, Scott AJ. Phylogenomic analysis of bacterial and archaeal sequences with AMPHORA2. Bioinformatics 2012; 28(7):1033-1034]
  
 
|}}
 
|}}

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