{"id":2278,"date":"2015-08-25T16:31:07","date_gmt":"2015-08-25T08:31:07","guid":{"rendered":"http:\/\/www.chenlianfu.com\/?p=2278"},"modified":"2015-08-25T16:31:07","modified_gmt":"2015-08-25T08:31:07","slug":"%e4%bd%bf%e7%94%a8-cafe-%e8%bf%9b%e8%a1%8c%e5%9f%ba%e5%9b%a0%e5%ae%b6%e6%97%8f%e6%89%a9%e5%bc%a0%e5%88%86%e6%9e%90","status":"publish","type":"post","link":"http:\/\/www.chenlianfu.com\/?p=2278","title":{"rendered":"\u4f7f\u7528 CAFE \u8fdb\u884c\u57fa\u56e0\u5bb6\u65cf\u6269\u5f20\u5206\u6790"},"content":{"rendered":"

1. CAFE \u7b80\u4ecb<\/h1>\n

CAFE<\/a> (Computational Analysis of gene Family Evolution) \u7528\u4e8e\u8fdb\u884c\u57fa\u56e0\u5bb6\u65cf\u7684\u6269\u5f20\u6536\u7f29\u5206\u6790\u3002<\/p>\n

2. CAFE \u4e0b\u8f7d\u548c\u5b89\u88c5<\/h1>\n
\r\n$ wget http:\/\/heanet.dl.sourceforge.net\/project\/cafehahnlab\/cafe.linux.x86_64\r\n$ wget http:\/\/downloads.sourceforge.net\/project\/cafehahnlab\/CAFEv3.1_Manual.pdf\r\n$ wget http:\/\/downloads.sourceforge.net\/project\/cafehahnlab\/CAFEv3.1_Manual.doc\r\n$ mv cafe.linux.x86_64 ~\/bin\/cafe\r\n$ cafe\r\n<\/pre>\n
3. CAFE \u7684\u7b80\u5355\u4f7f\u7528<\/h1>\n
CAFE \u9700\u8981\u7684\u8f93\u5165\uff1a<\/p>\n
\r\n1. \u57fa\u56e0\u5bb6\u65cf\u5728\u5404\u4e2a\u7269\u79cd\u4e2d\u7684\u6570\u76ee\u3002\u8be5\u6587\u4ef6\u5185\u5bb9\u6709\u591a\u884c\uff0c\u4ee5 tab \u5206\u5272\uff0c\u7b2c\u4e00\u884c\u5185\u5bb9\u5fc5\u987b\u5982\u4e0b\uff1a\r\nDescription    ID    species1    species2    ...\r\n\u4e0a\u9762 species1 \u548c species2 \u4e3a\u7269\u79cd\u540d\u7b80\u79f0\u3002\u540e\u9762\u7684\u884c\u4e3a\u76f8\u5e94\u7684\u503c\u3002 Description \u7684\u503c\u53ef\u4ee5\u7a7a\u7740\uff1b ID \u4e3a\u57fa\u56e0\u5bb6\u65cf\u7684\u540d\u79f0\uff1b\u5176\u5b83\u7684\u4e3a\u6570\u5b57\uff0c\u8868\u793a\u8be5\u57fa\u56e0\u5bb6\u65cf\u5728\u76f8\u5e94\u7269\u79cd\u4e2d\u7684\u6570\u76ee\u3002\r\n\u8be5\u6587\u4ef6\u53ef\u4ee5\u7531 OrthoMCL \u7684\u7ed3\u679c\u7edf\u8ba1\u5f97\u5230\u3002\r\n\r\n2. \u8d85\u5ea6\u91cf\u6811\uff0c\u679d\u957f\u8868\u793a\u5206\u6b67\u65f6\u95f4\u3002\u53ef\u4ee5\u4f7f\u7528 BEAST \u6216 r8s \u7b49\u751f\u6210\u3002\u6811\u4e2d\u7684\u7269\u79cd\u540d\u5fc5\u987b\u548c\u7b2c\u4e00\u4e2a\u6587\u4ef6\u4e2d\u7684\u7269\u79cd\u540d\u5bf9\u5e94\u3002\r\n\r\n3. \u8f93\u5165\u53c2\u6570  \u03bb \u7684\u503c\u3002\u8be5\u503c\u8868\u793a\u5728\u7269\u79cd\u8fdb\u5316\u8fc7\u7a0b\u4e2d\uff0c\u6bcf\u4e2a\u5355\u4f4d\u65f6\u95f4\u5185\u57fa\u56e0\u83b7\u5f97\u4e0e\u4e22\u5931\u7684\u6982\u7387\u3002\u53ef\u4ee5\u7531\u8f6f\u4ef6\u81ea\u5df1\u8fdb\u884c\u8ba1\u7b97\u3002\r\n<\/pre>\n
\u76f4\u63a5\u8f93\u5165\u547d\u4ee4 cafe \u5219\u8fdb\u5165\u4e86\u8f6f\u4ef6\u7684\u547d\u4ee4\u884c\u754c\u9762\uff0c\u4e5f\u53ef\u4ee5\u5c06\u547d\u4ee4\u5199\u5165\u5230 cafe \u811a\u672c\u4e2d\uff0c\u76f4\u63a5\u8fd0\u884c\u3002\u4e00\u4e2a\u7b80\u5355\u7684\u793a\u4f8b\u5982\u4e0b\uff1a<\/p>\n
\r\n#!~\/bin\/cafe\r\nversion\r\ndate\r\nload -i orthoMCL2cafe.tab -t 16 -l log.txt -p 0.05\r\ntree (((chimp:6,human:6):81,(mouse:17,rat:17):70):6,dog:93)\r\nlambda -s -t (((1,1)1,(2,2)2)2,2)\r\nreport out\r\n<\/pre>\n
\u4ee5\u4e0b\u7b80\u5355\u4ecb\u7ecd\u5982\u4e0a\u547d\u4ee4<\/p>\n
\r\nversion\r\n    \u663e\u793a\u8f6f\u4ef6\u7684\u7248\u672c\r\n\r\ndate\r\n    \u663e\u793a\u5f53\u524d\u65e5\u671f\r\n\r\nload\r\n    -i \u8f93\u5165\u7684\u6570\u636e\u6587\u4ef6\r\n    -t \u8bbe\u7f6e\u7a0b\u5e8f\u8fd0\u884c\u7684\u7ebf\u7a0b\u6570\uff0c\u9ed8\u8ba4\u4e3a 8\r\n    -l \u8bbe\u7f6e\u8f93\u51fa\u7684\u65e5\u5fd7\u6587\u4ef6\uff0c\u9ed8\u8ba4\u6807\u51c6\u8f93\u51fa\r\n    -p \u8bbe\u7f6e p_value \u7684\u9608\u503c\uff0c\u9ed8\u8ba4\u4e3a 0.01\r\n\r\ntree \u8f93\u5165\u8d85\u5ea6\u91cf\u6811\r\n\r\nlambda\r\n    -l \u8bbe\u7f6e \u03bb \u7684\u503c\r\n    -s \u8bbe\u7f6e\u8f6f\u4ef6\u81ea\u52a8\u5bfb\u627e\u6700\u4f18\u7684 \u03bb \u503c\r\n    -t \u9ed8\u8ba4\u4e0b\u6240\u6709\u5206\u652f\u7684 \u03bb \u503c\u662f\u76f8\u540c\u7684\uff0c\u82e5\u9700\u8981\u4e0d\u540c\u7684\u5206\u652f\u6709\u4e0d\u540c\u7684 \u03bb \u503c\uff0c\u5219\u7528\u8be5\u53c2\u6570\u8fdb\u884c\u8bbe\u7f6e\u3002\u8be5\u53c2\u6570\u7684\u503c\u548c tree \u547d\u4ee4\u4e2d\u7684\u6811\u7684\u5185\u5bb9\u4e00\u81f4\uff0c\u53ea\u662f\u53bb\u9664\u4e86\u5206\u6b67\u65f6\u95f4\uff0c\u5e76\u5c06\u7269\u79cd\u540d\u6362\u6210\u4e86\u8868\u793a \u03bb \u503c\u7684\u7f16\u53f7\u3002\u5176\u4e2d\uff0c\u76f8\u540c\u7684\u7f16\u53f7\u8868\u793a\u6709\u76f8\u540c\u7684 \u03bb \u503c\u3002\u4f8b\u5982\uff0c\u8be5\u53c2\u6570\u7684\u503c\u4e3a (((1,1)1,(2,2)2)2,2) \uff0c\u5b83\u8868\u793a chimp\uff0chuman \u548c \u7d27\u90bb\u7684\u5206\u652f\u6709\u76f8\u540c\u7684 \u03bb \u503c\uff0c\u5176\u5b83\u5206\u652f\u6709\u53e6\u5916\u76f8\u540c\u7684 \u03bb \u503c\u3002\r\n\r\nreport out\r\n    \u8bbe\u7f6e\u8f93\u51fa\u6587\u4ef6\u7684\u524d\u7f00\u4e3a out\r\n<\/pre>\n
4. CAFE \u7684\u8f93\u51fa\u7ed3\u679c<\/h1>\n
CAFE \u7684\u8f93\u51fa\u7ed3\u679c\u4e3a out.cafe\uff0c\u8be5\u6587\u4ef6\u5185\u5bb9\u5305\u542b\u5982\u4e0b\u51e0\u90e8\u5206\uff1a<\/p>\n
4.1 Tree<\/h2>\n
\u7b2c 1 \u884c\u4e3a\u8f93\u5165\u7684\u6811\u7684\u4fe1\u606f\u3002<\/p>\n
4.2 Lambda<\/h2>\n
\u7b2c 2 \u884c\u4e3a \u03bb \u503c\u3002<\/p>\n
4.3 \u8282\u70b9 ID<\/h2>\n
\u7b2c 3 \u884c\u4e3a\u8282\u70b9\u7684 ID\u3002\u540c\u6837\u662f\u6811\u7684\u6587\u5b57\u5185\u5bb9\uff0c\u4e0d\u8fc7\u7ed9\u6bcf\u4e2a\u8282\u70b9\u8fdb\u884c\u4e86\u7f16\u53f7\uff0c\u6709\u5229\u4e8e\u540e\u9762\u7684\u6570\u503c\u7684\u5bf9\u5e94\u3002<\/p>\n
4.4 \u6bcf\u4e2a\u57fa\u56e0\u5bb6\u65cf\u4e2d\u6269\u5f20\u6216\u6536\u7f29\u7684\u57fa\u56e0\u6570\u76ee<\/h2>\n
\u7b2c 4 \u884c\u7ed9\u51fa\u4e86\u4e00\u7cfb\u5217\u7684 \u8282\u70b9ID \u5bf9\u3002CAFE \u5bf9\u8fd9\u4e9b ID \u5bf9\u8fdb\u884c\u4e86\u57fa\u56e0\u5bb6\u65cf\u6269\u5f20\u7684\u7edf\u8ba1\u3002
\n\u7b2c 6 \u884c\u7684\u503c\u4e3a\u5e73\u5747\u6bcf\u4e2a\u57fa\u56e0\u5bb6\u65cf\u4e2d\u6269\u5f20\u7684\u57fa\u56e0\u6570\u76ee\uff0c\u8d1f\u6570\u8868\u793a\u57fa\u56e0\u5bb6\u65cf\u6536\u7f29\u3002<\/p>\n
4.5 \u57fa\u56e0\u5bb6\u65cf\u6570\u76ee<\/h2>\n
\u7b2c 7 \u884c\u7ed9\u51fa\u53d1\u751f\u4e86\u6269\u5f20\u7684\u57fa\u56e0\u5bb6\u65cf\u6570\u76ee\uff1b
\n\u7b2c 8 \u884c\u7ed9\u51fa\u6ca1\u6709\u53d1\u751f\u6539\u53d8\u7684\u57fa\u56e0\u5bb6\u65cf\u6570\u76ee\uff1b
\n\u7b2c 9 \u884c\u7ed9\u51fa\u53d1\u751f\u4e86\u6536\u7f29\u7684\u57fa\u56e0\u5bb6\u65cf\u6570\u76ee\uff1b<\/p>\n
4.6 \u6bcf\u4e2a\u57fa\u56e0\u5bb6\u65cf\u7684\u5177\u4f53\u6269\u5f20\u4e0e\u6536\u7f29\u60c5\u51b5<\/h2>\n
\u7b2c 10 \u884c\u4e4b\u540e\u662f\u6bcf\u4e2a\u57fa\u56e0\u5bb6\u65cf\u5177\u4f53\u7684\u6269\u5f20\u60c5\u51b5\u3002\u5176\u5185\u5bb9\u5206\u4e3a 4 \u5217\uff1a<\/p>\n
\r\n\u7b2c 1 \u5217\uff1a \u57fa\u56e0\u5bb6\u65cf ID\r\n\u7b2c 2 \u5217\uff1a \u6811\u7684\u4fe1\u606f\uff0c\u5176\u4e2d\u6bcf\u4e2a\u7269\u79cd\u540d\u540e\u9762\u591a\u4e2a\u4e00\u4e2a\u4e0b\u5212\u7ebf\u548c\u6570\u5b57\uff0c\u8be5\u6570\u5b57\u8868\u793a\u57fa\u56e0\u5bb6\u65cf\u7684\u6570\u76ee\u3002\u7279\u522b\u662f\u6bcf\u4e2a\u8282\u70b9\u7684\u57fa\u56e0\u5bb6\u65cf\u6570\u76ee\u90fd\u8ba1\u7b97\u51fa\u6765\u4e86\uff0c\u4ece\u800c\u77e5\u9053\u5728\u67d0\u4e00\u4e2a\u5206\u5316\u8fc7\u7a0b\u4e2d\u57fa\u56e0\u5bb6\u65cf\u7684\u6269\u5f20\u60c5\u51b5\u3002\r\n\u7b2c 3 \u5217\uff1a \u8be5\u57fa\u56e0\u5bb6\u65cf\u603b\u4f53\u4e0a\u7684\u6269\u5f20\u60c5\u51b5\u7684 p_value\uff0c\u4e0d\u540c\u7269\u79cd\u4e2d\u7684\u57fa\u56e0\u6570\u76ee\u5dee\u5f02\u8d8a\u5927\uff0c\u5219 p \u503c\u8d8a\u5c0f\u3002\r\n\u7b2c 4 \u5217\uff1a \u8ba1\u7b97\u51fa\u4e86\u6bcf\u4e2a\u5206\u679d\u7684\u57fa\u56e0\u5bb6\u65cf\u6269\u5f20\u7684\u663e\u8457\u6027\u3002\r\n<\/pre>\n
\u6839\u636e CAFE \u7684\u7ed3\u679c\uff0c\u53ef\u4ee5\u81ea\u884c\u7f16\u5199\u7a0b\u5e8f\u63d0\u53d6\u4fe1\u606f\u3002<\/p>\n","protected":false},"excerpt":{"rendered":"
1. CAFE \u7b80\u4ecb CAFE (Computational Analysis  … \u7ee7\u7eed\u9605\u8bfb →<\/span><\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":[],"categories":[3],"tags":[68],"_links":{"self":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2278"}],"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=2278"}],"version-history":[{"count":1,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2278\/revisions"}],"predecessor-version":[{"id":2279,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2278\/revisions\/2279"}],"wp:attachment":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=2278"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=2278"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=2278"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}