View source for MAFFT

[[Category:Software]][[Category:Bioinformatics]][[Category:Genomics]]
{|<!--CONFIGURATION: REQUIRED-->
|{{#vardefine:app|mafft}}
|{{#vardefine:url|http://mafft.cbrc.jp/alignment/software/}}
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|{{#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-->
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<!--Description-->
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{{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.
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==Environment Modules==
Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
==System Variables==
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
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{{#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.
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{{#if: {{#var: conf}}|==Configuration==
See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.
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{{#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)
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<!--Performance-->
{{#if: {{#var: testing}}|==Performance==
DOUBLE_CLICK_TO_WRITE_PERFORMANCE_TESTING_RESULTS_HERE
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<!--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
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<!--Installation-->
{{#if: {{#var: installation}}|==Installation==
See the [[{{PAGENAME}}_Install]] page for {{#var: app}} installation notes.|}}
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