Difference between revisions of "MAFFT"

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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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=MAFFT=
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[[Category:Software]][[Category:Bioinformatics]][[Category:Genomics]]
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{|<!--CONFIGURATION: REQUIRED-->
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|{{#vardefine:app|mafft}}
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|{{#vardefine:url|http://mafft.cbrc.jp/alignment/software/}}
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<!--CONFIGURATION: OPTIONAL (1=ON)-->
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|{{#vardefine:exe|1}} <!--RUNNING -->
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|{{#vardefine:conf|}} <!--CONFIGS-->
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|{{#vardefine:pbs|}} <!--PBS SCRIPTS-->
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|{{#vardefine:policy|}} <!--POLICY-->
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|{{#vardefine:testing|}} <!--TESTING/PROFILING-->
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|{{#vardefine:faq|}} <!--FAQ-->
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|{{#vardefine:citation|}} <!--CITATION-->
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|{{#vardefine:installation|}} <!--INSTALLATION-->
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|}
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<!--BODY-->
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<!--Description-->
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{{#if: {{#var: url}}|
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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.
 
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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<!--Modules-->
==Location==
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==Required Modules==
 
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[[Modules|modules documentation]]
Binaries are located in: /apps/mafft/<version>/bin/
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===Serial===
Version installed 9/9/11 is 6.859
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*{{#var:app}}
 
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==System Variables==
==Notes==
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* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
# 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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<!--Additional-->
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{{#if: {{#var: exe}}|==Additional Information==
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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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|}}
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<!--Configuration-->
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{{#if: {{#var: conf}}|==Configuration==
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See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.
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|}}
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<!--PBS scripts-->
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{{#if: {{#var: pbs}}|==PBS Script Examples==
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See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}}
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<!--Policy-->
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{{#if: {{#var: policy}}|==Usage Policy==
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WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used)
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|}}
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<!--Performance-->
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{{#if: {{#var: testing}}|==Performance==
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DOUBLE_CLICK_TO_WRITE_PERFORMANCE_TESTING_RESULTS_HERE
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|}}
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<!--Faq-->
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{{#if: {{#var: faq}}|==FAQ==
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*'''Q:''' **'''A:'''|}}
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<!--Citation-->
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{{#if: {{#var: citation}}|==Citation==
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If you publish research that uses {{#var:app}} you have to cite it as follows:
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DOUBLE_CLICK_TO_WRITE_CITATION_HERE
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|}}
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<!--Installation-->
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{{#if: {{#var: installation}}|==Installation==
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See the [[{{PAGENAME}}_Install]] page for {{#var: app}} installation notes.|}}
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__NOTOC____NOEDITSECTION__

Latest revision as of 21:21, 6 December 2019

Description

mafft website  

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

modules documentation

Serial

  • mafft

System Variables

  • HPC_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.