MAFFT: Difference between revisions
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Created page with "=MAFFT= MAFFT is a multiple sequence alignment program for unix-like operating systems. It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of <…" |
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= | [[Category:Software]][[Category:Bioinformatics]][[Category:Genomics]] | ||
{|<!--CONFIGURATION: REQUIRED--> | |||
|{{#vardefine:app|mafft}} | |||
|{{#vardefine:url|http://mafft.cbrc.jp/alignment/software/}} | |||
<!--CONFIGURATION: OPTIONAL (1=ON)--> | |||
|{{#vardefine:exe|1}} <!--RUNNING --> | |||
|{{#vardefine:conf|}} <!--CONFIGS--> | |||
|{{#vardefine:pbs|}} <!--PBS SCRIPTS--> | |||
|{{#vardefine:policy|}} <!--POLICY--> | |||
|{{#vardefine:testing|}} <!--TESTING/PROFILING--> | |||
|{{#vardefine:faq|}} <!--FAQ--> | |||
|{{#vardefine:citation|}} <!--CITATION--> | |||
|{{#vardefine:installation|}} <!--INSTALLATION--> | |||
|} | |||
<!--BODY--> | |||
<!--Description--> | |||
{{#if: {{#var: url}}| | |||
{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}} | |||
MAFFT is a multiple sequence alignment program for unix-like operating systems. It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of <∼200 sequences), FFT-NS-2 (fast; for alignment of <∼10,000 sequences), etc. | MAFFT is a multiple sequence alignment program for unix-like operating systems. It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of <∼200 sequences), FFT-NS-2 (fast; for alignment of <∼10,000 sequences), etc. | ||
<!--Modules--> | |||
== | ==Required Modules== | ||
[[Modules|modules documentation]] | |||
===Serial=== | |||
*{{#var:app}} | |||
==System Variables== | |||
== | * HPC_{{#uppercase:{{#var:app}}}}_DIR - installation directory | ||
<!--Additional--> | |||
{{#if: {{#var: exe}}|==Additional Information== | |||
MAFFT is compiled to run on multiple cores, use the --thread <cores> option to specify the number of cores to use. Make sure that this number corresponds to the resources requested in your #PBS -l nodes=1:ppn=<cores> statement. | |||
|}} | |||
<!--Configuration--> | |||
{{#if: {{#var: conf}}|==Configuration== | |||
See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details. | |||
|}} | |||
<!--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 (perhaps templates for a couple of main licensing schemes can be used) | |||
|}} | |||
<!--Performance--> | |||
{{#if: {{#var: testing}}|==Performance== | |||
DOUBLE_CLICK_TO_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: | |||
DOUBLE_CLICK_TO_WRITE_CITATION_HERE | |||
|}} | |||
<!--Installation--> | |||
{{#if: {{#var: installation}}|==Installation== | |||
See the [[{{PAGENAME}}_Install]] page for {{#var: app}} installation notes.|}} | |||
__NOTOC____NOEDITSECTION__ | |||
Revision as of 19:02, 10 August 2012
Description
MAFFT is a multiple sequence alignment program for unix-like operating systems. It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of <∼200 sequences), FFT-NS-2 (fast; for alignment of <∼10,000 sequences), etc.
Required Modules
Serial
- mafft
System Variables
- HPC_{{#uppercase:mafft}}_DIR - installation directory
Additional Information
MAFFT is compiled to run on multiple cores, use the --thread <cores> option to specify the number of cores to use. Make sure that this number corresponds to the resources requested in your #PBS -l nodes=1:ppn=<cores> statement.