{"id":3036,"date":"2019-10-25T01:00:29","date_gmt":"2019-10-24T17:00:29","guid":{"rendered":"http:\/\/www.chenlianfu.com\/?p=3036"},"modified":"2019-10-28T21:07:14","modified_gmt":"2019-10-28T13:07:14","slug":"%e4%bd%bf%e7%94%a8paml%e8%bd%af%e4%bb%b6%e5%88%a9%e7%94%a8%e5%af%86%e7%a0%81%e5%ad%90%e5%ba%8f%e5%88%97%e8%bf%9b%e8%a1%8c%e6%ad%a3%e9%80%89%e6%8b%a9%e5%88%86%e6%9e%90","status":"publish","type":"post","link":"http:\/\/www.chenlianfu.com\/?p=3036","title":{"rendered":"\u4f7f\u7528PAML\u8f6f\u4ef6\u5229\u7528\u5bc6\u7801\u5b50\u5e8f\u5217\u8fdb\u884c\u6b63\u9009\u62e9\u5206\u6790"},"content":{"rendered":"\n<p>PAML\u8f6f\u4ef6\u4e2d\u7684codeml\u547d\u4ee4\u53ef\u4ee5\u4f7f\u7528Maxmum Likelihood\u65b9\u6cd5\u5bf9\u5bc6\u7801\u5b50\u6216\u6c28\u57fa\u9178\u7684\u591a\u5e8f\u5217\u6bd4\u5bf9\u7ed3\u679c\u8fdb\u884c\u5206\u6790\u548c\u8fdb\u5316\u53c2\u6570\u8ba1\u7b97 \u3002\u8fd9\u4e24\u79cd\u6570\u636e\u5171\u7528\u4e00\u4e2a\u547d\u4ee4\uff0c\u7a0b\u5e8f\u8fd0\u884c\u65f6\u7684\u53c2\u6570\u7edd\u5927\u90e8\u5206\u662f\u516c\u7528\u7684\uff0c\u4f46\u4ecd\u9700\u8981\u5206\u6e05\u4e24\u79cd\u6570\u636e\u5404\u81ea\u7684\u53c2\u6570\u610f\u4e49\u3002PAML\u8f6f\u4ef6\u4e2d\u8fdb\u884c\u6b63\u9009\u62e9\u5206\u6790\u7684\u793a\u4f8b\u6570\u636e\u4f4d\u4e8eexamples\/lysozyme\/\u76ee\u5f55\u4e0b\u3002<\/p>\n\n\n\n<h2>1.\u8f93\u5165\u6587\u4ef6\uff081\/3\uff09\uff1a\u542b\u6709\u62d3\u6251\u7ed3\u6784\u7684\u6811\u6587\u4ef6<\/h2>\n\n\n\n<p>\u8f93\u5165 \u4e00\u4e2a\u6811\u6587\u4ef6input.trees\u3002\u8be5\u6587\u4ef6\u53ef\u4ee5\u662f\u6709\u6839\u6811\uff0c\u4e5f\u53ef\u4ee5\u662f\u65e0\u6839\u6811\uff0c\u4e5f\u53ef\u4ee5\u5e26\u6709\u679d\u957f\u4fe1\u606f\u3002codeml\u547d\u4ee4\u7528\u4e8e\u5206\u6790\u5404\u5206\u679d\u4e0a\u7684omega\u503c\uff0c\u82e5\u662f\u6709\u6839\u6811\u7684\u8bdd\uff0c\u5bf9\u4e8e\u5206\u6790root\u8282\u70b9\u6240\u5728\u7684\u5206\u679d\uff0c\u5176\u7ed3\u679c\u53ef\u80fd\u662f\u4e0d\u5bf9\u7684\u3002\u56e0\u6b64\uff0c\u4f5c\u8005\u63a8\u8350\u4f7f\u7528\u65e0\u6839\u6811\u8fdb\u884c\u6b63\u9009\u62e9\u5206\u6790\u3002\u65e0\u6839\u6811\u662f3\u5206\u53c9\u7684\u6811\uff0c\u6700\u5c11\u9700\u89813\u4e2a\u7269\u79cd\uff1b\u800c3\u4e2a\u7269\u79cd\u7684\u65e0\u6839\u6570\u67093\u4e2a\u5206\u679d\uff082n &#8211; 3\uff09\uff0c\u5bf9\u5176\u8fdb\u884c\u5206\u6790\uff0c\u4ec5\u80fd\u5f97\u5230\u67d0\u4e2a\u7269\u79cd\u6240\u5bf9\u5e94\u5206\u679d\u7684omega\u503c\uff0c\u8fd9\u79cd\u60c5\u51b5\u4e0b\u6ca1\u592a\u5927\u610f\u4e49\uff1b\u800c\u4f7f\u75284\u4e2a\u7269\u79cd\u7684\u65e0\u6839\u6811\u8fdb\u884c\u5206\u6790\uff0c\u53ef\u4ee5\u5f97\u5230\u4e24\u4e2a\u7269\u79cd\u5171\u540c\u7956\u5148\u5206\u679d\u7684omega\u503c\u3002\u6545\u4f5c\u8005\u63a8\u8350\u4f7f\u7528\u81f3\u5c114~5\u4e2a\u7269\u79cd\u8fdb\u884c\u5206\u6790\u3002\u4e00\u4e2a\u6811\u6587\u4ef6\u5185\u5bb9\u793a\u4f8b\uff1a <\/p>\n\n\n\n<pre class=\"wp-block-preformatted\">7  1<br>((Hsa_Human, Hla_gibbon) #1,((Cgu\/Can_colobus, Pne_langur) #1, Mmu_rhesus), (Ssc_squirrelM, Cja_marmoset));<br><\/pre>\n\n\n\n<p>\n\n\u6587\u4ef6\u5185\u5bb9\u5206\u4e24\u884c\uff1a\u7b2c\u4e00\u884c\u8868\u8ff0\u6811\u4e2d\u67095\u4e2a\u7269\u79cd\uff0c\u5171\u8ba11\u4e2a\u6811\uff0c\u4e24\u4e2a\u6570\u503c\u4e4b\u95f4\u7528\u4efb\u610f\u957f\u5ea6\u7684\u7a7a\u5206\u5272\u3002\u6b64\u5916\uff0cNewick\u683c\u5f0f\u7684\u6811\u5c3e\u90e8\u4e00\u5b9a\u8981\u6709\u5206\u53f7\uff0c\u6ca1\u6709\u7684\u8bdd\u7a0b\u5e8f\u53ef\u80fd\u4e0d\u80fd\u6b63\u5e38\u8fd0\u884c\u3002 \n\n<\/p>\n\n\n\n<h2>2. \u8f93\u5165\u6587\u4ef6\uff082\/3\uff09\uff1a\u5bc6\u7801\u5b50\u5e8f\u5217\u6bd4\u5bf9\u7ed3\u679c\u6587\u4ef6 input.txt<\/h2>\n\n\n\n<pre class=\"wp-block-preformatted\">7  390<br>Hsa_Human        AAGGTCTTTGAAAGGTGTGAGTTGGCCAGAACT...<br>Hla_gibbon       AAGGTCTTTGAAAGGTGTGAGTTGGCCAGAACT...<br>Cgu\/Can_colobus  AAGATCTTTGAAAGGTGTGAGTTGGCCAGAACT...<br>Pne_langur       AAGATCTTTGAAAGGTGTGAGTTGGCCAGAACT...<br>Mmu_rhesus       AAGATCTTTGAAAGGTGTGAGTTGGCCAGAACT...<br>Ssc_squirrelM    AAGGTCTTCGAAAGGTGTGAGTTGGCCAGAACT...<br>Cja_marmoset     AAGGTCTTTGAAAGGTGTGAGTTGGCCAGAACT...<\/pre>\n\n\n\n<p>PAML\u8981\u6c42\u8f93\u5165\u7684Phylip\u683c\u5f0f\uff0c\u5176\u7269\u79cd\u540d\u548c\u540e\u9762\u7684\u5e8f\u5217\u4e4b\u95f4\u81f3\u5c11\u95f4\u9694\u4e24\u4e2a\u7a7a\u683c\uff08\u662f\u4e3a\u4e86\u5141\u8bb8\u7269\u79cd\u540d\u7684\u5c5e\u540d\u548c\u79cd\u540d\u4e4b\u95f4\u6709\u4e00\u4e2a\u7a7a\u683c\uff09\u3002 <\/p>\n\n\n\n<h2>3. \u8f93\u5165\u6587\u4ef6\uff083\/3\uff09\uff1acodeml\u547d\u4ee4\u7684\u914d\u7f6e\u6587\u4ef6 codeml.ctl<\/h2>\n\n\n\n<p>\u8f6f\u4ef6\u96be\u70b9\u5728\u4e8e\u914d\u7f6e\u6587\u4ef6\u7684\u7406\u89e3\uff0c\u5e38\u7528\u793a\u4f8b\u5982\u4e0b\uff1a<\/p>\n\n\n\n<pre class=\"wp-block-preformatted\"><b>*\u8f93\u5165\u8f93\u51fa\u53c2\u6570\uff1a<\/b>\n      seqfile = input.txt    *\u8bbe\u7f6e\u8f93\u5165\u7684\u591a\u5e8f\u5217\u6bd4\u5bf9\u6587\u4ef6\u8def\u5f84\u3002\n     treefile = input.trees  *\u8bbe\u7f6e\u8f93\u5165\u7684\u6811\u6587\u4ef6\u8def\u5f84\u3002\n      outfile = mlc          *\u8bbe\u7f6e\u8f93\u51fa\u6587\u4ef6\u8def\u5f84\u3002\n        noisy = 9            *\u8bbe\u7f6e\u8f93\u51fa\u5230\u5c4f\u5e55\u4e0a\u7684\u4fe1\u606f\u91cf\u7b49\u7ea7\uff1a0\uff0c1\uff0c2\uff0c3\uff0c9\u3002\n      verbose = 0            *\u8bbe\u7f6e\u8f93\u51fa\u5230\u7ed3\u679c\u6587\u4ef6\u4e2d\u7684\u4fe1\u606f\u91cf\u7b49\u7ea7\uff1a0\uff0c\u7cbe\u7b80\u6a21\u5f0f\u7ed3\u679c\uff08\u63a8\u8350\uff09\uff1b1\uff0c\u8f93\u51fa\u8be6\u7ec6\u4fe1\u606f\uff0c\u5305\u542b\u78b1\u57fa\u5e8f\u5217\uff1b2\uff0c\u8f93\u51fa\u66f4\u591a\u4fe1\u606f\u3002\n        getSE = 0            *\u8bbe\u7f6e\u662f\u5426\u8ba1\u7b97\u5e76\u83b7\u5f97\u5404\u53c2\u6570\u7684\u6807\u51c6\u8bef\uff1a0\uff0c\u4e0d\u9700\u8981\uff1b1\uff0c\u9700\u8981\u3002\n RateAncestor = 0            *\u8bbe\u7f6e\u662f\u5426\u8ba1\u7b97\u5e8f\u5217\u4e2d\u6bcf\u4e2a\u4f4d\u70b9\u7684\u66ff\u6362\u7387\uff1a0\uff0c\u4e0d\u9700\u8981\uff1b1\uff0c\u9700\u8981\u3002\u5f53\u8bbe\u7f6e\u62101\u65f6\uff0c\u4f1a\u5728\u7ed3\u679c\u6587\u4ef6rates\u4e2d\u7ed9\u51fa\u5404\u4e2a\u4f4d\u70b9\u7684\u78b1\u57fa\u66ff\u6362\u7387\uff1b\u540c\u65f6\u4e5f\u4f1a\u8fdb\u884c\u7956\u5148\u5e8f\u5217\u7684\u91cd\u6784\uff0c\u5728\u7ed3\u679c\u6587\u4ef6rst\u4e2d\u6709\u4f53\u73b0\u3002\n\n<b>*\u6570\u636e\u4f7f\u7528\u8bf4\u660e\u53c2\u6570\uff1a<\/b>\n      runmode = 0      *\u8bbe\u7f6e\u7a0b\u5e8f\u83b7\u53d6\u8fdb\u5316\u6811\u62d3\u6251\u7ed3\u6784\u7684\u65b9\u6cd5\uff1a0\uff0c\u76f4\u63a5\u4ece\u8f93\u5165\u6587\u4ef6\u4e2d\u83b7\u53d6\u8fdb\u5316\u6811\u62d3\u6251\u7ed3\u6784\uff08\u63a8\u8350\uff09\uff1b1\uff0c\u7a0b\u5e8f\u4ee5\u8f93\u5165\u6587\u4ef6\u4e2d\u7684\u591a\u5206\u53c9\u6811\u4f5c\u4e3a\u8d77\u59cb\u6811\uff0c\u5e76\u4f7f\u7528\u661f\u72b6\u5206\u89e3\u6cd5\u641c\u7d22\u6700\u4f73\u6811\uff1b2\uff0c\u7a0b\u5e8f\u76f4\u63a5\u4ee5\u661f\u72b6\u6811\u4f5c\u4e3a\u8d77\u59cb\u6811\uff0c\u5e76\u4f7f\u7528\u661f\u72b6\u5206\u89e3\u6cd5\u641c\u7d22\u6700\u4f73\u6811\uff1b3\uff0c\u4f7f\u7528\u9010\u6b65\u6dfb\u52a0\u6cd5\u641c\u7d22\u6700\u4f73\u6811\uff1b4\uff0c\u4f7f\u7528\u7b80\u7ea6\u6cd5\u83b7\u53d6\u8d77\u59cb\u6811\uff0c\u518d\u8fdb\u884c\u90bb\u8fd1\u5206\u679d\u4ea4\u6362\u5bfb\u627e\u6700\u4f18\u6811\uff1b5\uff0c\u4ee5\u8f93\u5165\u6587\u4ef6\u4e2d\u7684\u6811\u4f5c\u4e3a\u8d77\u59cb\u6811\uff0c\u518d\u8fdb\u884c\u90bb\u8fd1\u5206\u679d\u4ea4\u6362\u5bfb\u627e\u6700\u4f18\u6811\uff1b-2\uff0c\u5bf9\u5bc6\u7801\u5b50\u5e8f\u5217\u8fdb\u884c\u4e24\u4e24\u6bd4\u8f83\u5e76\u4f7f\u7528ML\u65b9\u6cd5\u8ba1\u7b97DnDs\uff0c\u6216\u5bf9\u86cb\u767d\u5e8f\u5217\u8fdb\u884c\u4e24\u4e24\u6bd4\u8f83\u8ba1\u7b97ML\u8ddd\u79bb\uff0c\u800c\u4e0d\u8fdb\u884c\u5176\u5b83\u53c2\u6570\uff08\u679d\u957f\u548comega\u7b49\uff09\u7684\u8ba1\u7b97\u3002\n* fix_blength = 1      *\u8bbe\u7f6e\u7a0b\u5e8f\u5904\u7406\u8f93\u5165\u6811\u6587\u4ef6\u4e2d\u679d\u957f\u6570\u636e\u7684\u65b9\u6cd5\uff1a0\uff0c\u5ffd\u7565\u8f93\u5165\u6811\u6587\u4ef6\u4e2d\u7684\u679d\u957f\u4fe1\u606f\uff1b-1\uff0c\u4f7f\u7528\u4e00\u4e2a\u968f\u673a\u8d77\u59cb\u8fdb\u884c\u8fdb\u884c\u8ba1\u7b97\uff1b1\uff0c\u4ee5\u8f93\u5165\u7684\u679d\u957f\u4fe1\u606f\u4f5c\u4e3a\u521d\u59cb\u503c\u8fdb\u884cML\u8fed\u4ee3\u5206\u6790\uff0c\u6b64\u65f6\u9700\u8981\u6ce8\u610f\u8f93\u5165\u7684\u679d\u957f\u4fe1\u606f\u662f\u78b1\u57fa\u66ff\u6362\u7387\uff0c\u800c\u4e0d\u662f\u78b1\u57fa\u66ff\u6362\u6570\uff1b2\uff0c\u4e0d\u9700\u8981\u4f7f\u7528ML\u8fed\u4ee3\u8ba1\u7b97\u679d\u957f\uff0c\u76f4\u63a5\u4f7f\u7528\u8f93\u5165\u7684\u679d\u957f\u4fe1\u606f\uff0c\u9700\u8981\u6ce8\u610f\uff0c\u82e5\u679d\u957f\u4fe1\u606f\u548c\u5e8f\u5217\u4fe1\u606f\u4e0d\u543b\u5408\u53ef\u80fd\u5bfc\u81f4\u7a0b\u5e8f\u5d29\u6e83\uff1b3\uff0c\u8ba9ML\u8ba1\u7b97\u51fa\u7684\u679d\u957f\u548c\u8f93\u5165\u7684\u679d\u957f\u5448\u6b63\u6bd4\u3002\n      seqtype = 1      *\u8bbe\u7f6e\u8f93\u5165\u7684\u591a\u5e8f\u5217\u6bd4\u5bf9\u6570\u636e\u7684\u7c7b\u578b\uff1a1\uff0c\u5bc6\u7801\u5b50\u6570\u636e\uff1b2\uff0c\u6c28\u57fa\u9178\u6570\u636e\uff1b3\uff0c\u8f93\u5165\u6570\u636e\u867d\u7136\u4e3a\u5bc6\u7801\u5b50\u5e8f\u5217\uff0c\u4f46\u5148\u8f6c\u6362\u4e3a\u6c28\u57fa\u9178\u5e8f\u5217\u540e\u518d\u8fdb\u884c\u5206\u6790\u3002\n    CodonFreq = 2      *\u8bbe\u7f6e\u5bc6\u7801\u5b50\u9891\u7387\u7684\u8ba1\u7b97\u7b97\u6cd5\uff1a0\uff0c\u8868\u793a\u9664\u4e09\u79cd\u7ec8\u6b62\u5bc6\u7801\u5b50\u9891\u7387\u4e3a0\uff0c\u5176\u4f59\u5bc6\u7801\u503c\u9891\u7387\u5168\u90e8\u4e3a1\/61\uff1b1\uff0c\u7a0b\u5e8f\u5206\u522b\u8ba1\u7b97\u4e09\u4e2a\u5bc6\u7801\u5b50\u4f4d\u70b9\u7684\u56db\u79cd\u78b1\u57fa\u9891\u7387\uff0c\u518d\u7b97\u56db\u79cd\u78b1\u57fa\u9891\u7387\u5728\u4e09\u4e2a\u4f4d\u70b9\u4e0a\u7684\u7b97\u672f\u5e73\u5747\u503c\uff0c\u8ba1\u7b9761\u79cd\u5bc6\u7801\u5b50\u9891\u7387\u65f6\uff0c\u4f7f\u7528\u8be5\u5747\u503c\u8fdb\u884c\u8ba1\u7b97\uff0c\u8fd961\u79cd\u5bc6\u7801\u5b50\u9891\u7387\u4e4b\u548c\u4e0d\u7b49\u4e8e1\uff0c\u7136\u540e\u5bf9\u5176\u6570\u636e\u6807\u51c6\u5316\uff0c\u4f7f\u5176\u548c\u4e3a1\uff0c\u5f97\u5230\u6240\u6709\u5bc6\u7801\u5b50\u7684\u9891\u7387\uff1b2\uff0c\u7a0b\u5e8f\u5206\u522b\u8ba1\u7b97\u4e09\u4e2a\u5bc6\u7801\u5b50\u4f4d\u70b9\u7684\u56db\u79cd\u78b1\u57fa\u9891\u7387\uff0c\u8ba1\u7b9761\u79cd\u5bc6\u7801\u5b50\u9891\u7387\u65f6\uff0c\u4f7f\u7528\u76f8\u5e94\u4f4d\u70b9\u7684\u78b1\u57fa\u9891\u7387\u8fdb\u884c\u8ba1\u7b97\uff0c\u8fd961\u79cd\u5bc6\u7801\u5b50\u9891\u7387\u4e4b\u548c\u4e0d\u7b49\u4e8e1\uff0c\u7136\u540e\u5bf9\u5176\u6570\u636e\u6807\u51c6\u5316\uff0c\u4f7f\u5176\u548c\u4e3a1\uff0c\u5f97\u5230\u6240\u6709\u5bc6\u7801\u5b50\u7684\u9891\u7387\uff1b3\uff0c\u76f4\u63a5\u4f7f\u7528\u89c2\u6d4b\u5230\u7684\u5404\u5bc6\u7801\u5b50\u7684\u603b\u7684\u9891\u6570\/\u6240\u6709\u5bc6\u7801\u503c\u7684\u603b\u6570\uff0c\u5f97\u5230\u6240\u6709\u5bc6\u7801\u5b50\u7684\u9891\u7387\u3002\u4e00\u822c\u9009\u62e9\u7b2c\u4e09\u79cd\u65b9\u6cd5\uff0c\u8bbe\u7f6eCodonFre\u7684\u503c\u4e3a2\u3002\u7b2c\u4e00\u79cd\u65b9\u6cd5\u8ba9\u6240\u6709\u5bc6\u7801\u5b50\u9891\u7387\u76f8\u7b49\uff0c\u4e0d\u7b26\u5408\u5b9e\u9645\u8f7b\u5361\uff1b\u7b2c\u4e8c\u79cd\u65b9\u6cd5\u6ca1\u6709\u8003\u8651\u5230\u4e09\u79cd\u4f4d\u70b9\u5404\u78b1\u57fa\u9891\u7387\u7684\u5dee\u5f02\uff0c\u5f97\u5230\u7684\u5bc6\u7801\u5b50\u9891\u7387\u4e0d\u51c6\u786e\uff1b\u7b2c\u4e09\u79cd\u65b9\u6cd5\u80fd\u6bd4\u8f83\u51c6\u786e\u8ba1\u7b97\u51fa\u5404\u5bc6\u7801\u5b50\u7684\u9891\u7387\uff1b\u7b2c\u56db\u79cd\u65b9\u6cd5\u7531\u8f93\u5165\u6570\u636e\u5f97\u5230\u771f\u5b9e\u7684\u5404\u5bc6\u7801\u5b50\u9891\u7387\uff0c\u4f46\u6709\u65f6\u5019\u6709\u4e9b\u975e\u7ec8\u6b62\u5bc6\u7801\u5b50\u7684\u9891\u7387\u4e3a0\uff0c\u53ef\u80fd\u4e0d\u5229\u4e8e\u540e\u7eed\u7684\u8ba1\u7b97\u3002\n    cleandata = 1      *\u8bbe\u7f6e\u662f\u5426\u79fb\u9664\u4e0d\u660e\u786e\u5b57\u7b26\uff08N\u3001\uff1f\u3001W\u3001R\u548cY\u7b49\uff09\u6216\u542b\u4ee5\u540egap\u7684\u5217\u540e\u518d\u8fdb\u884c\u6570\u636e\u5206\u6790\uff1a0\uff0c\u4e0d\u9700\u8981\uff0c\u4f46\u5728\u5e8f\u5217\u4e24\u4e24\u6bd4\u8f83\u7684\u65f6\u5019\uff0c\u8fd8\u662f\u4f1a\u53bb\u9664\u540e\u8fdb\u884c\u6bd4\u8f83\uff1b1\uff0c\u9700\u8981\u3002\n*       ndata = 1      *\u8bbe\u7f6e\u8f93\u5165\u7684\u591a\u5e8f\u5217\u6bd4\u5bf9\u7684\u6570\u636e\u4e2a\u6570\u3002\n        clock = 0      *\u8bbe\u7f6e\u8fdb\u5316\u6811\u4e2d\u5404\u5206\u652f\u4e0a\u7684\u53d8\u5f02\u901f\u7387\u662f\u5426\u4e00\u81f4\uff0c\u670d\u4ece\u5206\u5b50\u949f\u7406\u8bba\uff1a0\uff0c\u53d8\u5f02\u901f\u7387\u4e0d\u4e00\u81f4\uff0c\u4e0d\u670d\u4ece\u5206\u5b50\u949f\u7406\u8bba\uff08\u5f53\u8f93\u5165\u6570\u636e\u4e2d\u7269\u79cd\u76f8\u5dee\u8f83\u8fdc\u65f6\uff0c\u5404\u5206\u652f\u53d8\u5f02\u901f\u7387\u4e0d\u4e00\u81f4\uff09\uff1b1\uff0c\u6240\u6709\u5206\u679d\u5177\u6709\u76f8\u540c\u7684\u53d8\u5f02\u901f\u7387\uff0c\u5168\u5c40\u4e0a\u670d\u4ece\u5206\u5b50\u949f\u7406\u8bba\uff1b2\uff0c\u8fdb\u5316\u6811\u5c40\u90e8\u7b26\u548c\u5206\u5b50\u949f\u7406\u8bba\uff0c\u7a0b\u5e8f\u8ba4\u4e3a\u9664\u4e86\u6307\u5b9a\u7684\u5206\u652f\u5177\u6709\u4e0d\u540c\u7684\u8fdb\u5316\u901f\u7387\uff0c\u5176\u5b83\u5206\u679d\u90fd\u5177\u6709\u76f8\u540c\u7684\u8fdb\u5316\u901f\u7387\uff0c\u8fd9\u8981\u6c42\u8f93\u5165\u7684\u8fdb\u5316\u6811\u4fe1\u606f\u4e2d\u4f7f\u7528#\u6765\u6307\u5b9a\u5206\u652f\uff1b3\uff0c\u5bf9\u591a\u57fa\u56e0\u6570\u636e\u8fdb\u884c\u8054\u5408\u5206\u6790\u3002\n        Mgene = 0      *\u8bbe\u7f6e\u662f\u5426\u6709\u591a\u4e2a\u57fa\u56e0\u7684\u591a\u5e8f\u5217\u6bd4\u5bf9\u4fe1\u606f\u8f93\u5165\uff0c\u4ee5\u53ca\u591a\u5404\u57fa\u56e0\u4e4b\u95f4\u7684\u53c2\u6570\u662f\u5426\u4e00\u81f4\uff1a0\uff0c\u8f93\u5165\u7684\u591a\u5e8f\u5217\u6bd4\u5bf9\u6587\u4ef6\u4e2d\u4ec5\u5305\u542b\u4e00\u4e2a\u57fa\u56e0\u65f6\uff0c\u6216\u591a\u4e2a\u57fa\u56e0\u5177\u6709\u76f8\u540c\u7684Kappa\u548cPi\u53c2\u6570\uff1b1\uff0c\u8f93\u5165\u6587\u4ef6\u5305\u542b\u591a\u4e2a\u57fa\u56e0\uff0c\u8fd9\u4e9b\u57fa\u56e0\u4e4b\u95f4\u662f\u76f8\u4e92\u72ec\u7acb\u7684\uff08\u8fd9\u4e9b\u57fa\u56e0\u4e4b\u95f4\u5177\u6709\u4e0d\u540c\u7684Kappa\u548cPi\u503c\uff0c\u4e14\u5176\u8fdb\u5316\u6811\u7684\u679d\u957f\u4e5f\u4e0d\u76f8\u5173\uff09\uff1b2\uff0c\u8f93\u5165\u6587\u4ef6\u5305\u542b\u591a\u4e2a\u57fa\u56e0\uff0c\u8fd9\u4e9b\u57fa\u56e0\u5177\u6709\u76f8\u540c\u7684Kappa\u503c\uff0c\u4e0d\u540c\u7684Pi\u503c\uff1b3\uff0c\u8f93\u5165\u6587\u4ef6\u5305\u542b\u591a\u4e2a\u57fa\u56e0\uff0c\u8fd9\u4e9b\u57fa\u56e0\u5177\u6709\u76f8\u540c\u7684Pi\u503c\uff0c\u4e0d\u540c\u7684Kappa\u503c\uff1b4\uff0c\u8f93\u5165\u6587\u4ef6\u5305\u542b\u591a\u4e2a\u57fa\u56e0\uff0c\u8fd9\u4e9b\u57fa\u56e0\u5177\u6709\u4e0d\u540c\u7684Kappa\u503c\u548c\u4e0d\u540c\u7684Pi\u503c\u3002\u5f53\u503c\u662f2\u30013\u62164\u65f6\uff0c\u591a\u4e2a\u57fa\u56e0\u7684\u8fdb\u5316\u6811\u679d\u957f\u867d\u7136\u957f\u5ea6\u4e0d\u4e00\u6837\uff0c\u4f46\u662f\u5448\u6b63\u6bd4\u5173\u7cfb\u3002\u8fd9\u70b9\u548c\u53c2\u6570\u503c\u7b49\u4e8e1\u662f\u4e0d\u4e00\u6837\u7684\u3002\n        icode = 0      *\u8bbe\u7f6e\u9057\u4f20\u5bc6\u7801\u3002\u5176\u503c1-10\u548cNCBI\u76841-11\u9057\u4f20\u5bc6\u7801\u89c4\u5219\u5bf9\u5e94\uff1a0\uff0c\u8868\u793a\u901a\u7528\u7684\u9057\u4f20\u5bc6\u7801\u3002\n   Small_Diff = .5e-6  *\u8bbe\u7f6e\u4e00\u4e2a\u5f88\u5c0f\u7684\u503c\uff0c\u4e00\u822c\u4f4d\u4e8e1e-8\u52301e-5\u4e4b\u95f4\u3002\u63a8\u8350\u68c0\u6d4b\u8bbe\u7f6e\u4e0d\u540c\u7684\u503c\u5728\u6bd4\u8f83\u5176\u7ed3\u679c\uff0c\u9700\u8981\u8be5\u53c2\u6570\u503c\u5bf9\u7ed3\u679c\u6ca1\u4ec0\u4e48\u5f71\u54cd\u3002\n\n<b>*\u4f4d\u70b9\u66ff\u6362\u6a21\u578b\u53c2\u6570\uff1a<\/b>\n        model = 1            *\u82e5\u8f93\u5165\u6570\u636e\u662f\u5bc6\u7801\u5b50\u5e8f\u5217\uff0c\u8be5\u53c2\u6570\u7528\u4e8e\u8bbe\u7f6ebranch models\uff0c\u5373\u8fdb\u5316\u6811\u5404\u5206\u679d\u7684omega\u503c\u7684\u5206\u5e03\uff1a0\uff0c\u8fdb\u5316\u6811\u4e0a\u6240\u6709\u5206\u679d\u7684omega\u503c\u4e00\u81f4\uff1b1\uff0c\u5bf9\u6bcf\u4e2a\u5206\u679d\u5355\u72ec\u8fdb\u884comega\u8ba1\u7b97\uff1b2\uff0c\u8bbe\u7f6e\u591a\u7c7bomega\u503c\uff0c\u6839\u636e\u6811\u6587\u4ef6\u4e2d\u5bf9\u5206\u679d\u7684\u7f16\u53f7\u4fe1\u606f\u6765\u786e\u5b9a\u7c7b\u522b\uff0c\u5177\u6709\u76f8\u540c\u7f16\u53f7\u7684\u5206\u679d\u5177\u6709\u76f8\u540c\u7684omega\u503c\uff0c\u6ca1\u6709\u7f16\u53f7\u7684\u5206\u679d\u5177\u6709\u76f8\u540c\u7684omega\u503c\uff0c\u7a0b\u5e8f\u5206\u522b\u8ba1\u7b97\u5404\u7f16\u53f7\u548c\u6ca1\u6709\u7f16\u53f7\u7684omega\u503c\u3002\n                             *\u82e5\u8f93\u5165\u6570\u636e\u662f\u86cb\u767d\u5e8f\u5217\uff0c\u6216\u6570\u636e\u662f\u5bc6\u7801\u5b50\u5e8f\u5217\u4e14seqtype\u503c\u662f3\u65f6\uff0c\u8be5\u53c2\u6570\u7528\u4e8e\u8bbe\u7f6e\u6c28\u57fa\u9178\u66ff\u6362\u6a21\u578b\uff1a0\uff0cPoisson\uff1b1\uff0c\u6c28\u57fa\u9178\u66ff\u6362\u7387\u548c\u6c28\u57fa\u9178\u7684\u89c2\u6d4b\u9891\u7387\u6210\u6b63\u6bd4\uff1b2\uff0c\u4eceaaRatefile\u53c2\u6570\u6307\u5b9a\u7684\u6587\u4ef6\u8def\u5f84\u4e2d\u8bfb\u53d6\u6c28\u57fa\u9178\u66ff\u6362\u7387\u4fe1\u606f\uff0c\u8fd9\u4e9b\u4fe1\u606f\u662f\u6839\u636e\u7ecf\u9a8c\u83b7\u5f97\uff0c\u5e76\u8bb0\u5f55\u5230\u540e\u7f00\u4e3a.dat\u7684\u914d\u7f6e\u6587\u4ef6\u4e2d\u3002\u8fd9\u4e9b\u7ecf\u9a8c\u6a21\u578b(Empirical Models)\u6587\u4ef6\u4f4d\u4e8ePAML\u8f6f\u4ef6\u5b89\u88c5\u76ee\u5f55\u4e2d\u7684dat\u76ee\u5f55\u4e0b\uff0c\u4f8b\u5982\uff0cDayhoff(dayhoff.dat)\u3001WAG(wag.dat)\u3001LG(lg.dat)\u3001mtMAN(mtman.dat)\u548cmtREV24(mtREV24.dat)\u7b49\uff1b\n   aaRatefile = dat\/wag.dat  *\u5f53\u5bf9\u86cb\u767d\u6570\u636e\u8fdb\u884c\u5206\u6790\uff0c\u4e14model = 2\u65f6\uff0c\u8be5\u53c2\u6570\u751f\u6548\uff0c\u7528\u4e8e\u8bbe\u7f6e\u6c28\u57fa\u9178\u66ff\u6362\u6a21\u578b\u3002\n       aaDist = 0            *\u8bbe\u7f6e\u6c28\u57fa\u9178\u4e4b\u95f4\u7684\u8ddd\u79bb\u3002\n      NSsites = 0            *\u8f93\u5165\u6570\u636e\u65f6\u5bc6\u7801\u5b50\u5e8f\u5217\u65f6\u751f\u6548\uff0c\u7528\u4e8e\u8bbe\u7f6esite model\uff0c\u5373\u5e8f\u5217\u5404\u4f4d\u70b9\u7684omega\u503c\u7684\u5206\u5e03\uff1a0\uff0c\u6240\u6709\u4f4d\u70b9\u5177\u6709\u76f8\u540c\u7684omega\u503c\uff1b1\uff0c\u5404\u4f4d\u70b9\u4e0a\u7684omega\u503c\u5c0f\u4e8e1\u6216\u7b49\u4e8e1\uff08\u670d\u4ece\u4e2d\u6027\u8fdb\u5316neutral\uff09\uff1b2\uff0c\u5404\u4f4d\u70b9\u4e0a\u7684omega\u503c\u5c0f\u4e8e1\u3001\u7b49\u4e8e1\u6216\u5927\u4e8e1\uff08\u9009\u62e9\u6027\u8fdb\u5316selection\uff09\uff1b3\uff0cdiscrete\uff1b4\uff0cfreq\uff1b5:gamma\uff1b6\uff0c2gamma\uff1b7\uff0cbeta\uff1b8\uff0cbeta&amp;w\uff1b9\uff0cbeta&amp;gamma\uff1b10\uff0cbeta&amp;gamma+1\uff1b11\uff0cbeta&amp;normal&gt;1\uff1b12\uff0c0&amp;2normal&gt;1\uff1b13\uff0c3normal&gt;0\u3002\n                             *\u53ef\u4ee5\u4e00\u6b21\u8f93\u5165\u591a\u4e2a\u6a21\u578b\u8fdb\u884c\u8ba1\u7b97\u5e76\u6bd4\u8f83\uff0c\u5176\u7ed3\u679c\u8f93\u51fa\u7684rst\u6587\u4ef6\u4e2d\u3002\n    fix_alpha = 1            *\u5e8f\u5217\u4e2d\u4e0d\u540c\u7684\u4f4d\u70b9\u5177\u6709\u4e0d\u540c\u7684\u78b1\u57fa\u66ff\u6362\u7387\uff0c\u670d\u4ecediscrete-gamma\u5206\u5e03\uff0c\u8be5\u6a21\u578b\u901a\u8fc7alpha\uff08shape\u53c2\u6570\uff09\u548cncatG\u53c2\u6570\u63a7\u5236\u3002\u8be5\u53c2\u6570\u8bbe\u7f6e\u662f\u5426\u7ed9\u5b9a\u4e00\u4e2aalpha\u503c\uff1a0\uff0c\u4f7f\u7528ML\u65b9\u6cd5\u5bf9alpha\u503c\u8fdb\u884c\u8ba1\u7b97\uff1b1\uff0c\u4f7f\u7528\u4e0b\u4e00\u4e2a\u53c2\u6570\u8bbe\u7f6e\u4e00\u4e2a\u56fa\u5b9a\u7684alpha\u503c\u3002\n\t                     *\u5bf9\u4e8e\u5bc6\u7801\u5b50\u5e8f\u5217\uff0c\u5f53NSsites\u53c2\u6570\u503c\u4e0d\u4e3a0\u6216model\u4e0d\u4e3a0\u65f6\uff0c\u63a8\u8350\u8bbe\u7f6efix_alpha = 1\u4e14alpha = 0\uff0c\u5373\u4e0d\u8bbe\u7f6ealpha\u503c\uff0c\u8ba4\u4e3a\u4f4d\u70b9\u95f4\u7684\u53d8\u5f02\u901f\u7387\u4e00\u81f4\uff0c\u5426\u5219\u7a0b\u5e8f\u62a5\u9519\u3002\u82e5\u8bbe\u7f6e\u4e86alpha\u503c\uff0c\u5219\u7a0b\u5e8f\u8ba4\u4e3a\u4e0d\u540c\u5bc6\u7801\u5b50\u4f4d\u70b9\u7684\u53d8\u5f02\u901f\u7387\u4e0d\u5747\u5300\uff0c\u4e14\u540c\u65f6\u6240\u6709\u4f4d\u70b9\u7684omega\u503c\u4e00\u81f4\uff0c\u5f53\u7136\u5404\u5206\u679d\u7684omega\u503c\u4e5f\u4f1a\u4e00\u81f4\uff0c\u8fd9\u65f6\u8981\u6c42NSsites\u548cmodel\u53c2\u6570\u503c\u90fd\u8bbe\u7f6e\u4e3a0\uff08\u8fd9\u4e00\u822c\u4e0d\u662f\u6211\u4eec\u9700\u8981\u7684\u5206\u6790\uff0c\u5b83\u4e0d\u80fd\u8fdb\u884c\u6b63\u9009\u62e9\u5206\u6790\u4e86\uff09\u3002\n        alpha = 0            *\u8bbe\u7f6e\u4e00\u4e2a\u56fa\u5b9a\u7684alpha\u503c\u6216\u521d\u59cbalpha\u503c\uff08\u63a8\u8350\u8bbe\u7f6e\u4e3a0.5\uff09\u3002\u8be5\u503c\u5c0f\u4e8e1\uff0c\u8868\u793a\u53ea\u6709\u5c11\u6570\u70ed\u70b9\u4f4d\u7f6e\u7684\u66ff\u6362\u7387\u8f83\u9ad8\uff1b\u8be5\u503c\u8d8a\u5c0f\uff0c\u8868\u793a\u4f4d\u70b9\u66ff\u6362\u7387\u5728\u5404\u4f4d\u70b9\u4e0a\u8d8a\u4e0d\u5747\u5300\uff1b\u82e5\u8bbe\u7f6efix_alpha = 1\u4e14alpha = 0\u5219\u8868\u793a\u6240\u6709\u4f4d\u70b9\u7684\u66ff\u6362\u7387\u662f\u6052\u5b9a\u4e00\u81f4\u7684\u3002\n       Malpha = 0            *\u5f53\u8f93\u5165\u7684\u591a\u5e8f\u5217\u6bd4\u5bf9\u7ed3\u679c\u4e2d\u6709\u591a\u57fa\u56e0\u65f6\uff0c\u8bbe\u7f6e\u8fd9\u4e9b\u57fa\u56e0\u95f4\u7684alpha\u503c\u662f\u5426\u76f8\u7b49\uff1a0\uff0c\u5206\u522b\u5bf9\u6bcf\u4e2a\u57fa\u56e0\u5355\u72ec\u8ba1\u7b97alpha\u503c\uff1b1\uff0c\u6240\u6709\u57fa\u56e0\u7684alpha\u503c\u4fdd\u6301\u4e00\u81f4\u3002\n        ncatG = 5            *\u5e8f\u5217\u4e2d\u4e0d\u540c\u4f4d\u70b9\u7684\u53d8\u5f02\u901f\u7387\u670d\u4eceGAMMA\u5206\u5e03\u7684\uff0cncatG\u662f\u5176\u4e00\u4e2a\u53c2\u6570\uff0c\u4e00\u822c\u8bbe\u7f6e\u4e3a5\uff0c4\uff0c8\u621610\uff0c\u4e14\u5e8f\u5217\u6761\u6570\u8d8a\u591a\uff0c\u8be5\u503c\u8bbe\u7f6e\u8d8a\u5927\u3002\n                             *\u5bf9\u4e8e\u5bc6\u7801\u5b50\u5e8f\u5217\uff0c\u5f53NSites\u8bbe\u7f6e\u4e3a3\u65f6\uff0cncatG\u8bbe\u7f6e\u4e3a3\uff1b\u5f53NSites\u8bbe\u7f6e\u4e3a4\u65f6\uff0cncatG\u8bbe\u7f6e\u4e3a5\uff1b\u5f53NSites\u503c\u8bbe\u7f6e&gt;=5\u65f6\uff0cncatG\u503c\u8bbe\u7f6e\u4e3a10\u3002\n    fix_kappa = 0            *\u8bbe\u7f6e\u662f\u5426\u7ed9\u5b9a\u4e00\u4e2aKappa\u503c\uff1a0\uff0c\u901a\u8fc7ML\u8fed\u4ee3\u6765\u4f30\u7b97Kappa\u503c\uff1b1\uff0c\u4f7f\u7528\u4e0b\u4e00\u4e2a\u53c2\u6570\u8bbe\u7f6e\u4e00\u4e2a\u56fa\u5b9a\u7684Kappa\u503c\u3002\n        kappa = 2            *\u8bbe\u7f6e\u4e00\u4e2a\u56fa\u5b9a\u7684Kappa\u503c\uff0c\u6216\u4e00\u4e2a\u521d\u59cb\u7684Kappa\u503c\u3002\n    fix_omega = 0            *\u8bbe\u7f6e\u662f\u5426\u7ed9\u5b9a\u4e00\u4e2aomega\u503c\uff1a0\uff0c\u901a\u8fc7ML\u8fed\u4ee3\u6765\u4f30\u7b97Kappa\u503c\uff1b1\uff0c\u4f7f\u7528\u4e0b\u4e00\u4e2a\u53c2\u6570\u8bbe\u7f6e\u4e00\u4e2a\u56fa\u5b9a\u7684omega\u503c\u3002 \n        omega = .4           *\u8bbe\u7f6e\u4e00\u4e2a\u56fa\u5b9a\u7684omega\u503c\uff0c\u6216\u4e00\u4e2a\u521d\u59cb\u7684omega\u503c\u3002\n       method = 0            *\u8bbe\u7f6e\u8bc4\u4f30\u679d\u957f\u7684ML\u8fed\u4ee3\u7b97\u6cd5\uff1a0\uff0c\u4f7f\u7528PAML\u7684\u8001\u7b97\u6cd5\u540c\u65f6\u8ba1\u7b97\u6240\u6709\u679d\u957f\uff0c\u5728clock = 0\u4e0b\u6709\u6548\uff1b1\uff0cPAML\u65b0\u52a0\u5165\u7684\u7b97\u6cd5\uff0c\u4e00\u6b21\u5bf9\u4e00\u4e2a\u679d\u957f\u8fdb\u884c\u8ba1\u7b97\uff0c\u8be5\u7b97\u6cd5\u4ec5\u5728clock\u53c2\u6570\u503c\u4e3a1\uff0c2\u62163\u4e0b\u5de5\u4f5c\u3002\n<\/pre>\n\n\n\n<h2>4. \u8fd0\u884ccodeml\u8fdb\u884c\u5206\u6790<\/h2>\n\n\n\n<p>\u8fd0\u884c\u7a0b\u5e8f\u7684\u547d\u4ee4\uff1a<\/p>\n\n\n\n<pre class=\"wp-block-code\"><code>codeml codeml.ctl<\/code><\/pre>\n\n\n\n<h2>5. \u6b63\u9009\u62e9\u57fa\u56e0\u5206\u6790<\/h2>\n\n\n\n<p>\u5bf9\u57fa\u56e0\u8fdb\u884c\u6b63\u9009\u62e9\u5206\u6790\uff0c\u53ef\u4ee5\u6309\u5982\u4e0b\u6b65\u9aa4\u8fdb\u884c\uff1a<\/p>\n\n\n\n<pre class=\"wp-block-preformatted\">(1) \u6536\u96c6\u8be5\u57fa\u56e0\u5728\u591a\u4e2a\u7269\u79cd\u4e2d\u7684CDS\u548cprotein\u5e8f\u5217\uff08\u53ef\u4ee5\u4f7f\u7528orthoMCL\u5206\u6790\u7ed3\u679c\uff09\u3002<br>(2) \u5bf9\u8be5\u57fa\u56e0\u7684\u86cb\u767d\u5e8f\u5217\u8fdb\u884c\u591a\u5e8f\u5217\u6bd4\u5bf9\uff0c\u518d\u6839\u636eCDS\u5e8f\u5217\u8f6c\u6362\u6210Codon\u5e8f\u5217\u6bd4\u5bf9\u7ed3\u679c\u3002\u8fd9\u4e2a\u6b65\u9aa4\u9700\u8981\u81ea\u5df1\u7f16\u5199\u4e00\u4e9b\u7a0b\u5e8f\u6765\u5b9e\u73b0\u3002<br>(3) \u6839\u636eCodon\u5e8f\u5217\u7684\u6bd4\u5bf9\u7ed3\u679c\u6784\u5efa\u7cfb\u7edf\u53d1\u80b2\u6811\u3002\u63a8\u8350\u4f7f\u7528RAxML\u8f6f\u4ef6\u4f7f\u7528ML\u7b97\u6cd5\u5bf9\u6240\u6709\u7684\u5355\u62f7\u8d1d\u540c\u6e90\u57fa\u56e0\u8fdb\u884c\u7269\u79cd\u6811\u6784\u5efa\u3002\u7136\u540e\uff0c\u8f93\u5165\u7269\u79cd\u6811\u4fe1\u606f\u3001Codon\u591a\u5e8f\u5217\u6bd4\u5bf9\u4fe1\u606f\uff0c\u4f7f\u7528codeml\u8fdb\u884comega\u8ba1\u7b97\u548c\u9009\u62e9\u538b\u6a21\u578b\u68c0\u9a8c\u3002<br>(4) \u5feb\u901f\u8fc7\u6ee4\u975e\u6b63\u9009\u62e9\u57fa\u56e0\uff1a\u8bbe\u7f6erunmode = -2\u8fd0\u884ccodeml\u547d\u4ee4\u5bf9\u4e24\u4e24\u5e8f\u5217\u6bd4\u8f83\uff0c\u4f7f\u7528ML\u65b9\u6cd5\u8ba1\u7b97dNdS\uff0c\u82e5\u5b58\u5728omega\u503c\u5927\u4e8e1\uff0c\u5219\u8ba4\u4e3a\u8be5\u57fa\u56e0\u53ef\u80fd\u5c5e\u4e8e\u6b63\u9009\u62e9\u57fa\u56e0\uff0c\u8fdb\u884c\u540e\u7eed\u5206\u6790\u3002<br>(5) \u6b63\u9009\u62e9\u57fa\u56e0\u7684\u521d\u6b65\u9274\u5b9a\u65b9\u6cd5\uff1a\u8bbe\u7f6emodel = 0\u3001NSsites = 1 2\u8fd0\u884ccodeml\u547d\u4ee4\uff08site models\uff09\u5206\u522b\u5bf9\u6b63\u9009\u62e9\u6a21\u578b(M2a)\u548c\u8fd1\u4e2d\u6027\u8fdb\u5316\u6a21\u578b(M1a)\u8fdb\u884c\u68c0\u6d4b\uff0c\u82e5\u4e24\u79cd\u6a21\u578b\u7684\u4f3c\u7136\u503c\u76f8\u5dee\u8f83\u5927\uff0c\u901a\u8fc7\u81ea\u7531\u5ea6\u4e3a2\u7684\u5361\u65b9\u68c0\u9a8c\uff0c\u53ef\u4ee5\u786e\u5b9a\u8be5\u57fa\u56e0\u662f\u5426\u4e3a\u6b63\u9009\u62e9\u57fa\u56e0\u3002\u4ece\u7a0b\u5e8f\u7ed3\u679c\u4e2d\uff08\u4f8b\u5982\uff1alnL(ntime: 11  np: 16):   -870.867266      +0.000000\uff09\u53ef\u4ee5\u627e\u5230M2a\u6a21\u578b\u7684\u4f3c\u7136\u503c<em>l<\/em><sub>1<\/sub>\u548cM1a\u6a21\u578b\u7684\u4f3c\u7136\u503c<em>l<\/em><sub>0<\/sub>\uff0c\u518d\u8ba1\u7b972\u0394<em>l<\/em>\u00a0= 2(<em>l<\/em><sub>1<\/sub>-<em>l<\/em><sub>0<\/sub>)\uff0c\u901a\u8fc7\u547d\u4ee4\u201cchi2 2 2\u0394<em>l<\/em>\u201d\u6839\u636e\u5361\u65b9\u68c0\u9a8c\u7b97\u51fap\u503c\u3002\u6b64\u5916\uff0c\u4e5f\u53ef\u4ee5\u8bbe\u7f6eNSsites = 7 8\u8fdb\u884c\u8ba1\u7b97\uff0c\u5219\u8868\u793a\u5206\u522b\u5bf9M8(beta &amp; omega)\u548cM7(beta)\u6a21\u578b\u8fdb\u884c\u68c0\u6d4b\uff0c\u548c\u524d\u8005\u7c7b\u4f3c\uff0c\u82e5\u4e24\u79cd\u6a21\u578b\u7684\u4f3c\u7136\u503c\u76f8\u5dee\u8f83\u5927\uff0c\u901a\u8fc7\u81ea\u7531\u5ea6\u4e3a2\u7684\u5361\u65b9\u68c0\u9a8c\uff0c\u53ef\u4ee5\u786e\u5b9a\u8be5\u57fa\u56e0\u662f\u5426\u4e3a\u6b63\u9009\u62e9\u57fa\u56e0\u3002\u6839\u636ePAML\u4f5c\u8005\u6240\u8bf4\uff0cM2a\u548cM1a\u7684\u6bd4\u8f83\uff0c\u6bd4M7-M8\u7684\u6bd4\u8f83\u66f4\u4e25\u683c\u3002\u5373\u82e5\u60f3\u5f97\u5230\u66f4\u591a\u7684\u6b63\u9009\u62e9\u57fa\u56e0\uff0c\u53ef\u4ee5\u4f7f\u7528M7_VS_M8\u5206\u6790\u3002\u6b64\u5916\uff0c\u6839\u636eM2\u548cM8\u6a21\u578b\u7684BEB\uff08Bayes empirical Bayes\uff09\u5206\u6790\u7ed3\u679c\uff0c\u8fd8\u53ef\u4ee5\u5f97\u5230\u5728\u591a\u5e8f\u5217\u6bd4\u5bf9\u7ed3\u679c\u4e2d\u7b2c\u4e00\u6761\u5e8f\u5217\u4e0a\u7684\u6b63\u9009\u62e9\u4f4d\u70b9\u3002\u6839\u636ePAML\u4f5c\u8005\u6240\u8bf4\uff0c\u8fd9\u79cdsite models\u4e4b\u95f4\u7684\u6bd4\u8f83\uff0c\u80fd\u7528\u4e8e\u68c0\u6d4b\u662f\u5426\u5728\u5e8f\u5217\u4e0a\u4e0d\u540c\u7684\u4f4d\u70b9\u5177\u6709\u4e0d\u540c\u7684omega\u503c\uff0c\u800c\u4e0d\u662f\u7528\u4e8e\u6b63\u9009\u62e9\u68c0\u6d4b\uff08We suggest that The M0-M3 comparison should be used as a test of variable <em>\u03c9<\/em> among sites rather than a test of positive selection\uff09\u3002<br>(6) \u6307\u5b9a\u5206\u5316\u679d\u4e0a\u7684\u6b63\u9009\u62e9\u57fa\u56e0\u9274\u5b9a\u65b9\u6cd5\uff1a\u7ecf\u8fc7\u4e0a\u4e00\u6b65\u521d\u6b65\u9274\u5b9a\u540e\uff0c\u8bbe\u7f6emodel = 2\u3001NSsites = 2\u3001fix_omega = 0\u3001omega = 2.0\u8fd0\u884ccodeml\u547d\u4ee4\uff08branch-site model A\uff09\uff1b\u518d\u8bbe\u7f6emodel = 2\u3001NSsites = 2\u3001fix_omega = 1\u3001omega = 1\u8fd0\u884ccodeml\u547d\u4ee4\uff08modified branch-site model A \/ null model\uff09\u3002\u8fdb\u884c\u8fd9\u4e24\u79cd\u6a21\u578b\u5206\u6790\u65f6\uff0c\u8981\u6c42\u8f93\u5165\u7684\u6811\u6587\u4ef6\u4e2d\u5bf9\u76ee\u6807\u5206\u5316\u679d\u8fdb\u884c\u6807\u6ce8\u3002\u5bf9\u8fd9\u4e24\u79cd\u6a21\u578b\u8fdb\u884cLRT\u5206\u6790\uff0c\u8ba1\u7b972\u0394<em>l<\/em>\u00a0= 2(<em>l<\/em><sub>1<\/sub>-<em>l<\/em><sub>0<\/sub>)\uff0c\u6ce8\u610f\u662f\u524d\u8005\u7684\u4f3c\u7136\u503c\u51cf\u540e\u8005\uff08null model\uff09\u7684\u4f3c\u7136\u503c\uff1b\u518d\u4f7f\u7528\u81ea\u7531\u5ea6\u4e3a1\u7684\u5361\u65b9\u68c0\u9a8c\uff0c\u901a\u8fc7\u547d\u4ee4\u201cchi2 1 2\u0394<em>l<\/em>\u201d\u8ba1\u7b97\u51fa\u7684\u503c\u518d\u9664\u4ee52\uff0c\u5373\u5f97\u5230p\u503c\u3002<br>(7) \u76ee\u6807\u5206\u5316\u679d\u4e0a\u7684\u5feb\u901f\u8fdb\u5316\u57fa\u56e0\uff08Rapidly evolving gene\uff09\u9274\u5b9a\u65b9\u6cd5\uff1a\u8bbe\u7f6emodel = 0\u3001NSsites = 0\u8fd0\u884ccodeml\u547d\u4ee4\uff0c\u518d\u8bbe\u7f6emodel = 2\u3001NSsites = 0\u8fd0\u884ccodeml\u547d\u4ee4\uff08\u8fd9\u65f6\u8981\u6c42\u8f93\u5165\u7684\u6811\u6587\u4ef6\u4e2d\u5bf9\u76ee\u6807\u5206\u5316\u679d\u8fdb\u884c\u6807\u6ce8\uff09\u3002\u7136\u540e\u6bd4\u8f83\u4e24\u79cd\u8fd0\u884c\u6a21\u5f0f\u4e0b\u7684\u4f3c\u7136\u503c\uff0c\u901a\u8fc7\u81ea\u7531\u5ea6\u4e3a1\u7684\u5361\u65b9\u68c0\u9a8c\uff0c\u53ef\u4ee5\u9274\u5b9a\u8be5\u57fa\u56e0\u5728\u76ee\u6807\u5206\u5316\u679d\u7684omega\u503c\u548c\u80cc\u666f\u5dee\u5f02\u663e\u8457\u3002<br><\/pre>\n\n\n\n<p><\/p>\n","protected":false},"excerpt":{"rendered":"<p>PAML\u8f6f\u4ef6\u4e2d\u7684codeml\u547d\u4ee4\u53ef\u4ee5\u4f7f\u7528Maxmum Likelihood\u65b9\u6cd5\u5bf9 &hellip; <a href=\"http:\/\/www.chenlianfu.com\/?p=3036\">\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\/3036"}],"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=3036"}],"version-history":[{"count":22,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/3036\/revisions"}],"predecessor-version":[{"id":3126,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/3036\/revisions\/3126"}],"wp:attachment":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=3036"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=3036"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=3036"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}