{"id":6282,"date":"2022-08-12T11:51:59","date_gmt":"2022-08-12T10:51:59","guid":{"rendered":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/?page_id=6282"},"modified":"2022-08-12T11:51:59","modified_gmt":"2022-08-12T10:51:59","slug":"mafft","status":"publish","type":"page","link":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/software\/applications\/mafft\/","title":{"rendered":"MAFFT"},"content":{"rendered":"<h2>Overview<\/h2>\n<p><a href=\"https:\/\/mafft.cbrc.jp\/alignment\/software\/\">MAFFT<\/a> 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 <\u223c200 sequences), FFT-NS-2 (fast; for alignment of <\u223c30,000 sequences), etc.\n\nVersions 7.505 with and without extensions are available.\n\n\n\n<h2>Restrictions on use<\/h2>\n<p>There are no restrictions on accessing this software on the CSF. The MAFFT without-extensions version is released under the <a href=\"https:\/\/mafft.cbrc.jp\/alignment\/software\/license.txt\"<BSD Lciense<\/a>. Please review the various <a href=\"https:\/\/mafft.cbrc.jp\/alignment\/software\/license66.txt\">MAFT with-extensions licenses<\/a> &#8211; this version of the app contains other public domain source codes which have their own licenses.<\/p>\n<p>Please cite your usage of this software using the information at the <a href=\"https:\/\/mafft.cbrc.jp\/alignment\/software\/#ref\">MAFFT References page<\/a>.<\/p>\n<h2>Set up procedure<\/h2>\n<p>We now recommend loading modulefiles within your jobscript so that you have a full record of how the job was run. See the example jobscript below for how to do this. Alternatively, you may load modulefiles on the login node and let the job <abbr title=\"add '#$ -V' to your jobscript\">inherit these settings<\/abbr>.<\/p>\n<p>Load one of the following modulefiles:<\/p>\n<pre>\r\nmodule load apps\/intel-19.1\/mafft\/7.505       # Without extensions version\r\nmodule load apps\/intel-19.1\/mafft\/7.505-ext   # With extensions version\r\n<\/pre>\n<h2>Running the application<\/h2>\n<p>Please do not run MAFFT on the login node. Jobs should be submitted to the compute nodes via batch. For hints and tips on running MAFFT please see their <a href=\"https:\/\/mafft.cbrc.jp\/alignment\/software\/tips0.html\">MAFFT &#8211; tips<\/a> page.<\/p>\n<h3>Serial batch job submission<\/h3>\n<p>Create a batch submission script (which will load the modulefile in the jobscript), for example:<\/p>\n<pre>\r\n#!\/bin\/bash --login\r\n#$ -cwd             # Job will run from the current directory\r\n                    # NO -V line - we load modulefiles in the jobscript\r\n\r\nmodule load apps\/intel-19.1\/mafft\/7.505\r\n\r\nmafft --thread $NSLOTS <em>args ...<\/em>\r\n<\/pre>\n<p>Submit the jobscript using: <\/p>\n<pre>qsub <em>scriptname<\/em><\/pre>\n<p>where <em>scriptname<\/em> is the name of your jobscript.<\/p>\n<h3>Parallel batch job submission<\/h3>\n<p>Create a batch submission script (which will load the modulefile in the jobscript), for example:<\/p>\n<pre>\r\n#!\/bin\/bash --login\r\n#$ -cwd             # Job will run from the current directory\r\n#$ -pe smp.pe 8     # Number of cores (can be 2--32)\r\n                    # NO -V line - we load modulefiles in the jobscript\r\n\r\nmodule load apps\/intel-19.1\/mafft\/7.505\r\n\r\nmafft --thread $NSLOTS <em>args ...<\/em>\r\n<\/pre>\n<p>Submit the jobscript using: <\/p>\n<pre>qsub <em>scriptname<\/em><\/pre>\n<p>where <em>scriptname<\/em> is the name of your jobscript.<\/p>\n<h2>Further info<\/h2>\n<ul>\n<li><a href=\"https:\/\/mafft.cbrc.jp\/alignment\/software\/manual\/manual.html\">MAFFT manual<\/a> (this does not seem to be updated for the most recent release).<\/li>\n<li><a href=\"https:\/\/mafft.cbrc.jp\/alignment\/software\/tips0.html\">MAFFT Tips<\/a>.<\/li>\n<li><a href=\"https:\/\/mafft.cbrc.jp\/alignment\/software\/\">MAFFT website<\/a>.<\/li>\n<\/ul>\n<h2>Updates<\/h2>\n<p>None.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Overview 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<\/p>\n","protected":false},"author":2,"featured_media":0,"parent":86,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-6282","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/6282","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/comments?post=6282"}],"version-history":[{"count":1,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/6282\/revisions"}],"predecessor-version":[{"id":6283,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/6282\/revisions\/6283"}],"up":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/86"}],"wp:attachment":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/media?parent=6282"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}