Difference between revisions of "Amphora2"
Jump to navigation
Jump to search
(4 intermediate revisions by 2 users not shown) | |||
Line 10: | Line 10: | ||
|{{#vardefine:testing|}} <!--PROFILING--> | |{{#vardefine:testing|}} <!--PROFILING--> | ||
|{{#vardefine:faq|}} <!--FAQ--> | |{{#vardefine:faq|}} <!--FAQ--> | ||
− | |{{#vardefine:citation|}} <!--CITATION--> | + | |{{#vardefine:citation|1}} <!--CITATION--> |
|{{#vardefine:installation|}} <!--INSTALLATION--> | |{{#vardefine:installation|}} <!--INSTALLATION--> | ||
|} | |} | ||
Line 23: | Line 23: | ||
<!--Modules--> | <!--Modules--> | ||
− | == | + | ==Environment Modules== |
− | + | Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | |
− | |||
− | |||
− | < | ||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
==System Variables== | ==System Variables== | ||
− | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory |
− | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_BIN - executable directory |
− | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_DOC - documentation directory |
− | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_EXE - test data directory |
− | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_TAX- taxonomy data directory |
− | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_TREE - tree data directory |
<!--Configuration--> | <!--Configuration--> | ||
Line 67: | Line 56: | ||
{{#if: {{#var: testing}}|==Performance== | {{#if: {{#var: testing}}|==Performance== | ||
− | + | ||
|}} | |}} | ||
Line 77: | Line 66: | ||
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: | ||
− | + | [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
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: