Difference between revisions of "Newick utils"
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(Created page with "Category:SoftwareCategory:BiologyCategory:Phylogenetics {|<!--CONFIGURATION: REQUIRED--> |{{#vardefine:app|newick_utils}} |{{#vardefine:url|https://github.com/tjun...") |
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|{{#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--> | ||
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{{#if: {{#var: url}}| | {{#if: {{#var: url}}| | ||
{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}} | {{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}} | ||
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| + | Original website: http://cegg.unige.ch/newick_utils | ||
| + | |||
| + | Archived: https://web.archive.org/web/20210409163921/http://cegg.unige.ch/newick_utils | ||
The Newick Utilities are a suite of programs for working with Newick-formatted | The Newick Utilities are a suite of programs for working with Newick-formatted | ||
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Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | 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_{{uc:{{#var:app}}}}_BIN - executable directory | ||
<!--Configuration--> | <!--Configuration--> | ||
{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
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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: | ||
| − | + | 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 | ||
|}} | |}} | ||
Latest revision as of 14:10, 1 September 2021
Description
Original website: http://cegg.unige.ch/newick_utils
Archived: https://web.archive.org/web/20210409163921/http://cegg.unige.ch/newick_utils
The Newick Utilities are a suite of programs for working with Newick-formatted phylogenetic trees.
Environment Modules
Run module spider newick_utils to find out what environment modules are available for this application.
System Variables
- HPC_NEWICK_UTILS_DIR - installation directory
- HPC_NEWICK_UTILS_BIN - executable directory
Citation
If you publish research that uses newick_utils 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
doi:10.1093/bioinformatics/btq243