Difference between revisions of "Newick-utils"

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(Created page with "Category:SoftwareCategory:BioinformaticsCategory:Phylogenetics {|<!--CONFIGURATION: REQUIRED--> |{{#vardefine:app|newickutils}} |{{#vardefine:url|http://cegg.unige...")
 
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[[Category:Software]][[Category:Bioinformatics]][[Category:Phylogenetics]]
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#REDIRECT [[Newick utils]]
{|<!--CONFIGURATION: REQUIRED-->
 
|{{#vardefine:app|newickutils}}
 
|{{#vardefine:url|http://cegg.unige.ch/newick_utils}}
 
<!--CONFIGURATION: OPTIONAL (|1}} means it's ON)-->
 
|{{#vardefine:conf|}}          <!--CONFIGURATION-->
 
|{{#vardefine:exe|}}            <!--ADDITIONAL INFO-->
 
|{{#vardefine:pbs|}}            <!--PBS SCRIPTS-->
 
|{{#vardefine:policy|}}        <!--POLICY-->
 
|{{#vardefine:testing|}}      <!--PROFILING-->
 
|{{#vardefine:faq|}}            <!--FAQ-->
 
|{{#vardefine:citation|1}}      <!--CITATION-->
 
|{{#vardefine:installation|}} <!--INSTALLATION-->
 
|}
 
<!--BODY-->
 
<!--Description-->
 
{{#if: {{#var: url}}|
 
{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}}
 
 
 
The Newick Utilities are a suite of Unix shell tools for processing phylogenetic trees. We distribute the package under the BSD License. Functions include re-rooting, extracting subtrees, trimming, pruning, condensing, drawing (ASCII graphics or SVG).
 
 
 
<!--Modules-->
 
==Required Modules==
 
===Serial===
 
* {{#var:app}}
 
<!--
 
===Parallel (OpenMP)===
 
* intel
 
* {{#var:app}}
 
===Parallel (MPI)===
 
* intel
 
* openmpi
 
* {{#var:app}}
 
-->
 
==System Variables==
 
* HPC_{{#uppercase:{{#var:app}}}}_DIR - installation directory
 
<!--Configuration-->
 
{{#if: {{#var: conf}}|==Configuration==
 
See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.
 
|}}
 
<!--Run-->
 
{{#if: {{#var: exe}}|==Additional Information==
 
 
 
WRITE_ADDITIONAL_INSTRUCTIONS_ON_RUNNING_THE_SOFTWARE_IF_NECESSARY
 
 
 
|}}
 
<!--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:
 
 
 
The Newick Utilities: High-throughput Phylogenetic tree Processing in the UNIX Shell. ''Thomas Junier and Evgeny M. Zdobnov''. Bioinformatics 2010 26:1669-1670
 
 
 
[http://bioinformatics.oxfordjournals.org/content/26/13/1669.full http://bioinformatics.oxfordjournals.org/content/26/13/1669.full]
 
 
 
doi:10.1093/bioinformatics/btq243
 
 
 
|}}
 
<!--Installation-->
 
{{#if: {{#var: installation}}|==Installation==
 
See the [[{{PAGENAME}}_Install]] page for {{#var: app}} installation notes.|}}
 
<!--Turn the Table of Contents and Edit paragraph links ON/OFF-->
 
__NOTOC____NOEDITSECTION__
 

Latest revision as of 14:25, 1 September 2021

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