{"id":2217,"date":"2014-07-07T21:27:21","date_gmt":"2014-07-07T13:27:21","guid":{"rendered":"http:\/\/www.chenlianfu.com\/?p=2217"},"modified":"2014-07-07T21:30:13","modified_gmt":"2014-07-07T13:30:13","slug":"%e4%bd%bf%e7%94%a8-prottest-%e6%9d%a5%e9%80%89%e6%8b%a9%e6%9c%80%e4%bc%98%e6%b0%a8%e5%9f%ba%e9%85%b8%e6%9b%bf%e4%bb%a3%e6%a8%a1%e5%9e%8b","status":"publish","type":"post","link":"http:\/\/www.chenlianfu.com\/?p=2217","title":{"rendered":"\u4f7f\u7528 ProtTest \u6765\u9009\u62e9\u6700\u4f18\u6c28\u57fa\u9178\u66ff\u4ee3\u6a21\u578b"},"content":{"rendered":"<h1>1. ProtTest \u7b80\u4ecb<\/h1>\n<p>ProtTest \u7528\u6765\u8fdb\u884c\u6700\u4f18\u6c28\u57fa\u9178\u66ff\u4ee3\u6a21\u578b\u7684\u9009\u62e9\u3002\u76f8\u5e94\u7684\uff0c\u9002\u7528\u4e8e\u6838\u82f7\u9178\u7684\u8f6f\u4ef6\u662f jModeltest\u3002<br \/>\nProtTest \u901a\u8fc7 PhyML \u5bf9\u8fdb\u5316\u6811\u548c\u6a21\u578b\u53c2\u6570\u7684\u6700\u5927\u4f3c\u7136\u4f30\u8ba1\uff0c\u901a\u8fc7 AIC, BIC \u5206\u503c\u6216 DT \u6765\u5bfb\u627e\u6700\u4f73\u6a21\u578b\u3002\u5206\u503c\u8d8a\u5c0f\u8d8a\u4f18\u3002<br \/>\nProTest 3.2 \u7248\u672c\u5305\u542b 15 \u79cd\u4e0d\u540c\u7c7b\u578b\u7684 rate matrices\uff1b\u8003\u8651\u5230\u4f4d\u70b9\u7684 rate variation (+I: invariable sites; +G: gamma-distributed rates) \u548c observed amino acid frequencies (+F), \u5171\u6709 120 \u79cd\u4e0d\u540c\u7684\u6a21\u578b\u3002<br \/>\nProtTest \u5b98\u7f51\uff1a<a href=\"https:\/\/code.google.com\/p\/prottest3\/\" target=\"_blank\">https:\/\/code.google.com\/p\/prottest3\/<\/a><br \/>\n\u4ece\u6b64\u5904\u4e0b\u8f7d\u8be5\u8f6f\u4ef6\u3002\u53ef\u80fd\u9700\u8981\u8bbe\u7f6e\u4ee3\u7406\u540e\u4e0b\u8f7d\u3002<br \/>\n\u53c2\u8003\u6587\u732e\uff1a<a href=\"http:\/\/bioinformatics.oxfordjournals.org\/content\/27\/8\/1164\" target=\"_blank\">ProtTest 3: fast selection of best-fit models of protein evolution<\/a><\/p>\n<h1>2. ProtTest \u4e0b\u8f7d\u548c\u5b89\u88c5<\/h1>\n<pre>\r\n$ tar zxf prottest-3.4-20140123.tar.gz -C \/opt\/biosoft\r\n$ cd \/opt\/biosoft\/prottest-3.4-20140123\r\n$ echo 'export PROTTEST_HOME=\/opt\/biosoft\/prottest-3.4-20140123' >> ~\/.bashrc\r\n\u67e5\u770b\u8bf4\u660e\u6587\u6863\uff1a\r\n$ less README\r\n<\/pre>\n<h1>3. ProtTest \u7684\u4f7f\u7528<\/h1>\n<p>ProtTest \u4f7f\u7528 JAVA \u7f16\u5199\uff0c\u6709\u56fe\u5f62\u5316\u548c\u547d\u4ee4\u884c\u4e24\u79cd\u8fd0\u884c\u6a21\u5f0f\u3002<\/p>\n<h2>3.1 \u56fe\u5f62\u5316\u754c\u9762\u4f7f\u7528<\/h2>\n<pre>\r\n\u5fc5\u987b\u8981\u8fdb\u5165\u5230\u7a0b\u5e8f\u7684\u6240\u5728\u7684\u76ee\u5f55\u8fd0\u884c\u7a0b\u5e8f\u4ee5\u542f\u52a8\u56fe\u5f62\u5316\u754c\u9762\r\n$ cd \/opt\/biosoft\/prottest-3.4-20140123\/runXProtTestHPC.sh\r\n$ runXProtTestHPC.sh\r\n<\/pre>\n<p>\u542f\u52a8 JAVA \u754c\u9762\u540e\uff0c\u70b9\u51fb File&#8211;Load Alignment, \u4e0a\u4f20\u591a\u5e8f\u5217\u6bd4\u5bf9\u7ed3\u679c\uff1b\u7136\u540e\u70b9\u51fb Analysis&#8211;Compute likehood scores, \u9009\u62e9\u6240\u4f7f\u7528\u7684\u7ebf\u7a0b\u6570\uff0c\u4ee5\u53ca\u5019\u9009\u6a21\u578b\u7684\u9009\u62e9\uff0c\u548c\u8ba1\u7b97 likelihood \u7684 topology\uff1b\u7136\u540e\u70b9\u51fb Compute, \u8fdb\u884c\u8ba1\u7b97\uff0c\u6240\u9700\u8981\u6d88\u8017\u7684\u5b9e\u9645\u6709\u70b9\u957f\uff1b\u8ba1\u7b97\u5b8c\u6bd5\u540e\uff0c\u70b9\u51fb Selection&#8211;Results \u6765\u67e5\u770b\u7ed3\u679c\u3002\u901a\u8fc7 AIC, BIC, AICc \u548c DT \u6765\u67e5\u770b\u5176\u5f97\u5206\uff0c\u70b9\u51fb\u8868\u683c\u7684\u7b2c1\u884c\u8fdb\u884c\u6392\u5e8f\uff0c\u5bfb\u627e\u5206\u503c\u6700\u5c0f\u7684\u6a21\u578b\u4f5c\u4e3a\u6700\u4f18\u6c28\u57fa\u9178\u66ff\u4ee3\u6a21\u578b\u3002<\/p>\n<h2>3.2 \u547d\u4ee4\u884c\u8fd0\u884c<\/h2>\n<p>\u5e38\u7528\u4f8b\u5b50\uff1a<\/p>\n<pre>\r\n\u4e0d\u52a0\u53c2\u6570\u8fd0\u884c\uff0c\u5219\u7ed9\u51fa\u5e2e\u52a9\u6587\u6863\uff1a\r\njava -jar \/opt\/biosoft\/prottest-3.4-20140123\/prottest-3.4.jar\r\n\r\n\u5e38\u7528\u7684\u547d\u4ee4\u884c\uff1a\r\njava -jar \/opt\/biosoft\/prottest-3.4-20140123\/prottest-3.4.jar -i proteins.phy -all-distributions -F -AIC -BIC -tc 0.5 -threads 24 -o prottest.out\r\n<\/pre>\n<p>ProtTest \u7684\u5e38\u7528\u53c2\u6570\uff1a<\/p>\n<pre>\r\n-i alignment_filename\r\n\u5fc5\u987b\u53c2\u6570\uff0c\u8f93\u5165\u591a\u5e8f\u5217\u6bd4\u5bf9\u7ed3\u679c\u6587\u4ef6\u3002\r\n-o output_filename\r\n\u8f93\u51fa\u7684\u6587\u4ef6\u540d\u3002\u4e0d\u8bbe\u7f6e\uff0c\u5219\u9ed8\u8ba4\u8f93\u51fa\u5230\u6807\u51c6\u8f93\u51fa\u3002\r\n-[matrix]\r\n\u6307\u5b9a\u9700\u8981\u5206\u6790\u7684 matrix \u3002 \u8be5 matrix \u53ef\u4ee5\u88ab\u66ff\u6362\u4e3a JTT LG DCMut MtREV MtMam MtArt Dayhoff WAG RtREV CpREV Blosum62 VT HIVb HIVw FLU \u8fd9 15 \u79cd matrix\u3002 \u82e5\u4e0d\u6307\u5b9a\uff0c\u5219\u9ed8\u8ba4\u5168\u9009\u3002\r\n-all-distributions\r\n\u6307\u5b9a matrix \u6a21\u578b\u7ed3\u5408 I \u6216 G \u6216 I+G\r\n-F\r\n\u6307\u5b9a matrix \u6a21\u578b\u7ed3\u5408 empirical frenquency estimation\r\n-AIC\r\n\u8f93\u51fa\u7ed3\u679c\u4e2d\u6309 AIC (Akaike Information Criterion) \u6392\u5e8f\r\n-BIC\r\n\u8f93\u51fa\u7ed3\u679c\u4e2d\u6309 BIC (Bayesian Information Criterion) \u6392\u5e8f\r\n-AICC\r\n\u8f93\u51fa\u7ed3\u679c\u4e2d\u6309 AICc (Corrected Akaike Information Criterion) \u6392\u5e8f\r\n-DT\r\n\u8f93\u51fa\u7ed3\u679c\u4e2d\u6309 DT (Decision Theory Criterion) \u6392\u5e8f\r\n-tc consensus_threshold\r\n\u8f93\u51fa\u6ee1\u8db3\u6307\u5b9a\u9608\u503c\u7684\u4e00\u81f4\u6811\u3002\u8be5\u503c\u5728 0.5~ 1.0 \u4e4b\u95f4\u3002[0.5 = majority rule consensus ; 1.0 = strict consensus]\r\n-threads number_of_threads\r\n\u4f7f\u7528\u7684 CPU \u6570\u3002\r\n<\/pre>\n","protected":false},"excerpt":{"rendered":"<p>1. ProtTest \u7b80\u4ecb ProtTest \u7528\u6765\u8fdb\u884c\u6700\u4f18\u6c28\u57fa\u9178\u66ff\u4ee3\u6a21\u578b\u7684\u9009\u62e9 &hellip; <a href=\"http:\/\/www.chenlianfu.com\/?p=2217\">\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\/2217"}],"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=2217"}],"version-history":[{"count":3,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2217\/revisions"}],"predecessor-version":[{"id":2220,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2217\/revisions\/2220"}],"wp:attachment":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=2217"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=2217"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=2217"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}