{"id":2214,"date":"2014-07-07T15:21:05","date_gmt":"2014-07-07T07:21:05","guid":{"rendered":"http:\/\/www.chenlianfu.com\/?p=2214"},"modified":"2014-07-16T23:46:22","modified_gmt":"2014-07-16T15:46:22","slug":"%e4%bd%bf%e7%94%a8-mafft-%e8%bf%9b%e8%a1%8c%e5%a4%9a%e5%ba%8f%e5%88%97%e6%af%94%e5%af%b9","status":"publish","type":"post","link":"http:\/\/www.chenlianfu.com\/?p=2214","title":{"rendered":"\u4f7f\u7528 MAFFT \u8fdb\u884c\u591a\u5e8f\u5217\u6bd4\u5bf9"},"content":{"rendered":"<h1>1. MAFFT \u7b80\u4ecb<\/h1>\n<p>\u6700\u7ecf\u5178\u548c\u5e7f\u4e3a\u719f\u77e5\u7684\u591a\u5e8f\u5217\u6bd4\u5bf9\u8f6f\u4ef6\u662f clustalw \u3002 \u4f46\u662f\u73b0\u6709\u7684\u591a\u5e8f\u5217\u6bd4\u5bf9\u8f6f\u4ef6\u8f83\u591a\uff0c\u6709\u6587\u732e\u62a5\u9053\uff1a\u6bd4\u5bf9\u901f\u5ea6\uff08Muscle>MAFFT>ClustalW>T-Coffee\uff09\uff0c\u6bd4\u5bf9\u51c6\u786e\u6027\uff08MAFFT>Muscle>T-Coffee>ClustalW\uff09\u3002\u56e0\u6b64\uff0c\u63a8\u8350\u4f7f\u7528 MAFFT \u8f6f\u4ef6\u8fdb\u884c\u591a\u5e8f\u5217\u6bd4\u5bf9\u3002<\/p>\n<h1>2. MAFFT \u4e0b\u8f7d\u5b89\u88c5<\/h1>\n<pre>\r\n$ wget http:\/\/mafft.cbrc.jp\/alignment\/software\/mafft-7.158-without-extensions-src.tgz\r\n$ tar zxf mafft-7.158-without-extensions-src.tgz\r\n$ cd mafft-7.158-without-extensions\/core\r\n$ perl -p -i -e 's#PREFIX =.*#PREFIX = \/opt\/biosoft\/mafft#' Makefile\r\n$ perl -p -i -e 's#BINDIR =.*#BINDIR = \/opt\/biosoft\/mafft\/bin\/#' Makefile\r\n$ make\r\n$ make install\r\n$ echo 'PATH=$PATH:\/opt\/biosoft\/mafft\/bin\/' >> ~\/.bashrc\r\n$ source ~\/.bashrc\r\n\r\n\u68c0\u6d4b\u8f6f\u4ef6\u662f\u5426\u6b63\u786e\u5b89\u88c5\r\n$ cd ..\/test\r\n$ rehash                                                   # if necessary\r\n$ mafft sample > test.fftns2                               # FFT-NS-2\r\n$ mafft --maxiterate 100  sample > test.fftnsi             # FFT-NS-i\r\n$ mafft --globalpair sample > test.gins1                   # G-INS-1\r\n$ mafft --globalpair --maxiterate 100  sample > test.ginsi # G-INS-i\r\n$ mafft --localpair sample > test.lins1                    # L-INS-1\r\n$ mafft --localpair --maxiterate 100  sample > test.linsi  # L-INS-i\r\n$ diff test.fftns2 sample.fftns2\r\n$ diff test.fftnsi sample.fftnsi\r\n$ diff test.gins1 sample.gins1\r\n$ diff test.ginsi sample.ginsi\r\n$ diff test.lins1 sample.lins1\r\n\u82e5 diff \u7684\u7ed3\u679c\u4e0d\u6362\u56de\u5f02\u5e38\uff0c\u5219\u6b63\u786e\u5b89\u88c5\u3002\r\n<\/pre>\n<h1>3. MAFFT \u4f7f\u7528<\/h1>\n<p>MAFFT \u6709\u4e00\u4e9b\u53c2\u6570\uff0c\u9002\u5408\u4e0d\u540c\u60c5\u51b5\u4e0b\u7684\u591a\u5e8f\u5217\u6bd4\u5bf9\u3002<br \/>\n\u8f6f\u4ef6\u8f93\u5165\u4e3a FASTA \u683c\u5f0f\uff0c\u9ed8\u8ba4\u8f93\u51fa\u5230\u6807\u51c6\u8f93\u51fa\u3002<\/p>\n<h2>3.1 \u8f83\u4e3a\u7cbe\u786e\u7684\u65b9\u6cd5<\/h2>\n<h3>L-INS-i<\/h3>\n<p>\u6700\u51c6\u786e\u7684\u65b9\u6cd5\u3002\u9002\u5408\u4e8e <200 \u6761\u5e8f\u5217\uff0c\u4e14\u5e8f\u5217\u957f\u5ea6 <~2000 aa\/nt \u7684\u6bd4\u5bf9\u3002\n\n\n<pre>\r\n$ mafft &#8211;localpair &#8211;maxiterate 1000 input [> output]\r\n$ linsi input [> output]\r\n<\/pre>\n<h3>G-INS-i<\/h3>\n<p>\u9002\u5408\u4e8e\u5e8f\u5217\u957f\u5ea6\u76f8\u4f3c\u7684\u591a\u5e8f\u5217\u6bd4\u5bf9\u3002\u5e8f\u5217\u6761\u6570 <200, \u5e8f\u5217\u957f\u5ea6 <~2000 aa\/nt \u3002\n\n\n<pre>\r\n$ mafft &#8211;globalpair &#8211;maxiterate 1000 input [> output]\r\n$ ginsi input [> output]\r\n<\/pre>\n<h3>E-INS-i<\/h3>\n<p>\u9002\u5408\u5e8f\u5217\u4e2d\u5305\u542b\u8f83\u5927\u7684\u975e\u5339\u914d\u533a\u57df\u3002\u5e8f\u5217\u6761\u6570 <200, \u5e8f\u5217\u957f\u5ea6 <~2000 aa\/nt \u3002\n\n\n<pre>\r\n$ mafft &#8211;ep 0 &#8211;genafpair &#8211;maxiterate 1000 input [> output]\r\n$ einsi input [> output]\r\n<\/pre>\n<h2>3.2 \u8282\u7ea6\u901f\u5ea6\u7684\u65b9\u6cd5<\/h2>\n<h3>FFT-NS-i<\/h3>\n<p>\u51cf\u5c11\u8fed\u4ee3\u6b21\u6570\uff0c\u6700\u5927\u8fed\u4ee3\u6b21\u6570\u51cf\u4e3a 2 \u3002<\/p>\n<pre>\r\n$ mafft --retree 2 --maxiterate 2 input [> output]\r\n$ fftnsi input [> output]\r\n<\/pre>\n<h3>FFT-NS-2<\/h3>\n<p>\u6700\u5927\u8fed\u4ee3\u6b21\u6570\u51cf\u4e3a 0 \u3002<\/p>\n<pre>\r\n$ mafft --retree 2 --maxiterate 0 input [> output]\r\n$ fftns input [> output]\r\n<\/pre>\n<h3>FFT-NS-1<\/h3>\n<p>\u6b64\u65b9\u6cd5\u975e\u5e38\u5feb\u901f\uff0c\u9002\u5408 >2000 \u6761\u5e8f\u5217\u7684\u591a\u5e8f\u5217\u6bd4\u5bf9\u3002<\/p>\n<pre>\r\n$ mafft --retree 1 --maxiterate 0 input [> output]\r\n<\/pre>\n<h3>NW-NS-i<\/h3>\n<p>\u8fed\u4ee3\u8fc7\u7a0b\u4e2d\u4e0d\u8fdb\u884c FFT aproximation<\/p>\n<pre>\r\n$ mafft --retree 2 --maxiterate 2 --nofft input [> output]\r\n$ nwnsi input [> output]\r\n<\/pre>\n<h3>NW-NS-2<\/h3>\n<pre>\r\n$ mafft --retree 2 --maxiterate 0 --nofft input [> output]\r\n$ nwns input [> output]\r\n<\/pre>\n<h3>NW-NS-PartTree-1<\/h3>\n<p>3 \u4e2a\u53c2\u6570\u90fd\u8bbe\u7f6e\u4e3a\u6700\u4e0d\u6d88\u8017\u65f6\u95f4\u7684\u7c7b\u578b\uff0c\u9002\u5408\u4e8e ~10,000 \u5230 ~50,000 \u6761\u5e8f\u5217\u7684\u6bd4\u5bf9\u3002<\/p>\n<pre>\r\n$ mafft --retree 1 --maxiterate 0 --nofft --parttree input [> output]\r\n<\/pre>\n","protected":false},"excerpt":{"rendered":"<p>1. MAFFT \u7b80\u4ecb \u6700\u7ecf\u5178\u548c\u5e7f\u4e3a\u719f\u77e5\u7684\u591a\u5e8f\u5217\u6bd4\u5bf9\u8f6f\u4ef6\u662f clustalw \u3002 &hellip; <a href=\"http:\/\/www.chenlianfu.com\/?p=2214\">\u7ee7\u7eed\u9605\u8bfb <span class=\"meta-nav\">&rarr;<\/span><\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":[],"categories":[1],"tags":[],"_links":{"self":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2214"}],"collection":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=2214"}],"version-history":[{"count":2,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2214\/revisions"}],"predecessor-version":[{"id":2245,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2214\/revisions\/2245"}],"wp:attachment":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=2214"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=2214"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=2214"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}