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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| − | = | + | [[Category:Software]][[Category:Biology]][[Category:Sequencing]] |
| + | {|<!--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--> | |
| − | == | + | ==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 | |
| − | + | <!--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__ | ||
Latest revision as of 20:23, 15 August 2022
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.
Environment Modules
Run module spider mafft to find out what environment modules are available for this application.
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.