{"id":2974,"date":"2019-10-21T20:21:45","date_gmt":"2019-10-21T12:21:45","guid":{"rendered":"http:\/\/www.chenlianfu.com\/?p=2974"},"modified":"2019-10-27T14:38:45","modified_gmt":"2019-10-27T06:38:45","slug":"%e4%bd%bf%e7%94%a8paml%e8%bf%9b%e8%a1%8c%e5%88%86%e6%ad%a7%e6%97%b6%e9%97%b4%e8%ae%a1%e7%ae%97","status":"publish","type":"post","link":"http:\/\/www.chenlianfu.com\/?p=2974","title":{"rendered":"\u4f7f\u7528PAML\u8fdb\u884c\u5206\u6b67\u65f6\u95f4\u8ba1\u7b97"},"content":{"rendered":"\n

PAML\u8f6f\u4ef6\u4e2d\u7684mcmctree\u547d\u4ee4\u53ef\u4ee5\u4f7f\u7528Bayesian\u65b9\u6cd5\u4f30\u7b97\u7269\u79cd\u5206\u6b67\u65f6\u95f4\u3002\u5bf9\u7a0b\u5e8f\u8f93\u5165\u5e26\u6709\u6821\u51c6\u70b9\u4fe1\u606f\u7684\u6709\u6839\u6811\u3001\u591a\u5e8f\u5217\u6bd4\u5bf9\u7ed3\u679c\uff0c\u5373\u53ef\u5f97\u5230\u8fdb\u5316\u6811\u5404\u5185\u90e8\u8282\u70b995%\u7f6e\u4fe1\u533a\u95f4\u5206\u6b67\u65f6\u95f4\u4fe1\u606f\u3002PAML\u8f6f\u4ef6\u4e5f\u80fd\u5229\u7528\u5e26\u6709\u679d\u957f\u4fe1\u606f\u7684\u6811\uff0c\u5feb\u901f\u8fdb\u884c\u5206\u6b67\u65f6\u95f4\u8ba1\u7b97\u3002PAML\u8f6f\u4ef6\u4e2d\u7684\u7ec3\u4e60\u6570\u636e\u4f4d\u4e8e\u6587\u4ef6\u5939 install_path\/paml4.9i\/examples\/DatingSoftBound\u76ee\u5f55\u4e0b\u3002\u8be6\u7ec6\u8bf4\u660e\u6587\u6863\uff1a http:\/\/abacus.gene.ucl.ac.uk\/software\/MCMCtree.Tutorials.pdf<\/a> <\/p>\n\n\n\n

1. \u8f93\u5165\u6587\u4ef6\uff081\/3\uff09\uff1a\u5e26\u6709\u6821\u51c6\u70b9\u7684\u6709\u6839\u6811 input.trees<\/h2>\n\n\n\n

\u8f93\u5165\u4e00\u4e2a\u5e26\u6709\u6821\u51c6\u70b9\u7684\u6709\u6839\u6811\u6587\u4ef6\uff0c\u793a\u4f8b\u5982\u4e0b\uff1a<\/p>\n\n\n\n

7 1
((((human, (chimpanzee, bonobo)) '>.06<.08', gorilla), (orangutan, sumatran)) '>.12<.16', gibbon);<\/pre>\n\n\n\n
\u6587\u4ef6\u5185\u5bb9\u5206\u4e24\u884c\uff1a\u7b2c\u4e00\u884c\u8868\u8ff0\u6811\u4e2d\u67097\u4e2a\u7269\u79cd\uff0c\u5171\u8ba11\u4e2a\u6811\uff0c\u4e24\u4e2a\u6570\u503c\u4e4b\u95f4\u7528\u7a7a\u5206\u5272\uff1b\u7b2c\u4e8c\u884c\u5219\u662fNewick\u683c\u5f0f\u6811\u4fe1\u606f\uff0c\u5176\u4e2d\u5305\u542b\u6709\u6821\u51c6\u70b9\u4fe1\u606f\u3002\u6821\u51c6\u70b9\u4fe1\u606f\u4e00\u822c\u630795%HPD\uff08Highest Posterior Density\uff09\u5bf9\u5e94\u7684\u7f6e\u4fe1\u533a\u95f4\uff1b\u6821\u51c6\u70b9\u5355\u4f4d\u662f100MYA\uff08\u8f6f\u4ef6\u8bf4\u660e\u6587\u6863\u4e2d\u4f7f\u7528\u8be5\u5355\u4f4d\uff0c\u4e5f\u63a8\u8350\u4f7f\u7528\u8be5\u5355\u4f4d\uff0c\u82e5\u4f7f\u7528\u5176\u5b83\u5355\u4f4d\uff0c\u540e\u7eed\u914d\u7f6e\u6587\u4ef6\u4e2d\u7684\u76f8\u5173\u53c2\u6570\u4e5f\u9700\u8981\u5bf9\u5e94\u4fee\u6539\uff09\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<\/p>\n\n\n\n
2. \u8f93\u5165\u6587\u4ef6\uff082\/3\uff09\uff1a\u5bc6\u7801\u5b50\u57283\u4e2a\u4f4d\u70b9\u7684\u591a\u5e8f\u5217\u6bd4\u5bf9\u7ed3\u679c\uff08Phylip\u683c\u5f0f\uff09 input.txt<\/h2>\n\n\n\n
7  3331\nhuman               AGACTGTTAGCAGCGCCGGGCAACTCCCTACTCAA...\nchimpanzee          AGACTGTTGGCAACGTCGGGCAACTCCCCGCCCAA...\nbonobo              AGACTGTTGGCAACGCCGGGCAACTCCCCGCCCAA...\ngorilla             AGATTGTTAGCAACGTCGGGTAACCCCCCACTCAA...\norangutan           AGGCTACTAACAGCGCCGGACGATTCCTCGCCTAA...\nsumatran            AGACTACTAACAGCGCCGGGCGATTCCTCACCCAA...\ngibbon              AGACTATTGACAACGTCGGGCAACTCTCTACTCAA...\n7  3331\nhuman               AAATTCCTTCCCTTGTCCCTTTTTTCCTTTCATTA...\nchimpanzee          AAATTCCTCCCCTTGTCCCTTTTTTCCTTTCATTA...\nbonobo              AAATTCCTCCCCTTGTCCCTTTTTTCCTTTCATTA...\ngorilla             AAATTCCTTCCCTTGTCCCTTTTTTCCTTTCATTA...\norangutan           AAATTCCTCCCCTTGTCCCTTTTTTCCTTTCATTA...\nsumatran            AAGTTCCTTCCCTTGTCCCTTTTTTCCTTTCATTA...\ngibbon              AAATTCCTCCCCTTGTCCCTCTTTTCCTTTCATTA...\n7  3331\nhuman               CATGCTACTCCACACACCAAGCTATCTAGCCTCCC...\nchimpanzee          CATACTACTCCACACACCAAACTACCTAGCCTCCC...\nbonobo              CATGCTACTCCACACACCAAGCTACCTAGTCTCCC...\ngorilla             CATACTACTCCACACACCAAATCATCTAGCCTCCC...\norangutan           CATACCACTCCACACCCTATACCATCCAACTTCCC...\nsumatran            CATATCACTCCAAACCCCAAACCATCCAGCCTCCC...\ngibbon              CATACTACTCCATACACCAAATTATCCAACTCCCC...<\/code><\/pre>\n\n\n\n
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
\u5f53\u7136\uff0c\u4e5f\u53ef\u4ee5\u8f93\u5165\u4e00\u4e2a\u591a\u5e8f\u5217\u6bd4\u5bf9\u7ed3\u679c\u8fdb\u884c\u5206\u6790\u3002\u5728\u8f6f\u4ef6\u8bf4\u660e\u6587\u6863\u4e2d\uff0c\u662f\u5bc6\u7801\u5b50\u4e09\u4e2a\u4f4d\u70b9\u5206\u522b\u7684\u591a\u5e8f\u5217\u6bd4\u5bf9\u7ed3\u679c\uff0c\u7a0b\u5e8f\u53ef\u4ee5\u5206\u522b\u8ba1\u7b97\u5bc6\u7801\u5b50\u5404\u4e2a\u4f4d\u70b9\u7684\u53d8\u5f02\u901f\u7387\u3002<\/p>\n\n\n\n
\u6b64\u5916\uff0c\u4e5f\u53ef\u4ee5\u8f93\u5165\u5bc6\u7801\u5b50\u6216\u6c28\u57fa\u9178\u5e8f\u5217\u6bd4\u5bf9\u4fe1\u606f\uff0c\u5219\u9700\u8981\u518d\u914d\u7f6e\u6587\u4ef6\u4e2d\u4fee\u6539\u76f8\u5e94\u7684\u53c2\u6570\u6765\u8868\u660e\u6570\u636e\u7c7b\u578b\u3002\u82e5\u4f7f\u7528\u6c28\u57fa\u9178\u5e8f\u5217\u6765\u8fdb\u884c\u5206\u6790\uff0c\u7531\u4e8emcmctree\u547d\u4ee4\u4e0d\u80fd\u9009\u62e9\u8f83\u597d\u7684\u6c28\u57fa\u9178\u66ff\u6362\u6a21\u578b\u8fdb\u884c\u5206\u6790\uff0c\u9700\u8981\u81ea\u5df1\u624b\u52a8\u8fd0\u884ccodeml\u8fdb\u884c\u5206\u6790\u540e\uff0c\u5728\u751f\u6210\u4e2d\u95f4\u6587\u4ef6\u7528\u4e8e\u8fd0\u884cmcmctree\uff0c\u6bd4\u8f83\u9ebb\u70e6\u3002\u56e0\u6b64\uff0c\u63a8\u8350\u6309\u4e0a\u8ff0\u65b9\u6cd5\u4f7f\u7528\u5bc6\u7801\u5b50\u4e09\u4f4d\u70b9\u7684\u78b1\u57fa\u5e8f\u5217\u4f5c\u4e3a\u8f93\u5165\u4fe1\u606f\u8fdb\u884cPAML\u5206\u6790\u3002<\/p>\n\n\n\n
3. \u8f93\u5165\u6587\u4ef6\uff083\/3\uff09\uff1amcmctree\u547d\u4ee4\u7684\u914d\u7f6e\u6587\u4ef6 mcmctree.ctl<\/h2>\n\n\n\n
\u8f6f\u4ef6\u96be\u70b9\u5728\u4e8e\u914d\u7f6e\u6587\u4ef6\u7684\u7406\u89e3\uff0c\u793a\u4f8b\u5982\u4e0b\uff1a<\/p>\n\n\n\n
\n*\u8f93\u5165\u8f93\u51fa\u53c2\u6570\uff1a<\/b>\n        seed = -1           *\u8bbe\u7f6e\u4e00\u4e2a\u968f\u673a\u6570\u6765\u8fd0\u884c\u7a0b\u5e8f\u3002\u82e5\u8bbe\u7f6e\u4e3a-1\uff0c\u8868\u793a\u4f7f\u7528\u7cfb\u7edf\u5f53\u524d\u65f6\u95f4\u4e3a\u968f\u673a\u6570\u3002\n     seqfile = input.txt    *\u8bbe\u7f6e\u8f93\u5165\u7684\u591a\u5e8f\u5217\u6bd4\u5bf9\u6587\u4ef6\u8def\u5f84\n    treefile = input.trees  *\u8bbe\u7f6e\u8f93\u5165\u7684\u5e26\u6821\u51c6\u70b9\u4fe1\u606f\u6709\u6839\u6811\u7684\u6587\u4ef6\u8def\u5f84 \n    mcmcfile = mcmc.txt     *\u8bbe\u7f6e\u8f93\u51fa\u7684mcmc\u4fe1\u606f\u6587\u672c\u6587\u4ef6\uff0c\u53ef\u4ee5\u7528Tracer\u8f6f\u4ef6\u67e5\u770b\n     outfile = out.txt      *\u8bbe\u7f6e\u8f93\u51fa\u6587\u4ef6\u8def\u5f84\uff0c\u8be5\u6587\u4ef6\u4e2d\u8bb0\u5f55\u4e86\u8d85\u5ea6\u91cf\u6811\u548c\u8fdb\u5316\u901f\u7387\u7b49\u53c2\u6570\u4fe1\u606f\u3002\n\n*\u6570\u636e\u4f7f\u7528\u8bf4\u660e\u53c2\u6570\uff1a<\/b>\n       ndata = 3         *\u8bbe\u7f6e\u8f93\u5165\u7684\u591a\u5e8f\u5217\u6bd4\u5bf9\u7684\u6570\u636e\u4e2a\u6570\u3002\u8fd9\u91cc\u6307\u5bc6\u7801\u5b503\u4e2a\u4f4d\u7f6e\u7684\u6570\u636e\u3002\n     seqtype = 0         *\u8bbe\u7f6e\u591a\u5e8f\u5217\u6bd4\u5bf9\u7684\u6570\u636e\u7c7b\u578b\uff1a0\uff0c\u8868\u793a\u6838\u9178\u6570\u636e\uff1b1\uff0c\u8868\u793a\u5bc6\u7801\u5b50\u6bd4\u5bf9\u6570\u636e\uff1b2\uff0c\u8868\u793a\u6c28\u57fa\u9178\u6570\u636e\u3002\u6839\u636e\u4e0d\u540c\u7684\u6570\u636e\u7c7b\u578b\uff0c\u7a0b\u5e8f\u8c03\u7528\u76f8\u5e94\u7684baseml\u6216codeml\u8fdb\u884c\u76f8\u5e94\u7684\u53c2\u6570\u8ba1\u7b97\u3002\n     usedata = 1         *\u8bbe\u7f6e\u662f\u5426\u5229\u7528\u591a\u5e8f\u5217\u6bd4\u5bf9\u7684\u6570\u636e\uff1a0\uff0c\u8868\u793a\u4e0d\u4f7f\u7528\u591a\u5e8f\u5217\u6bd4\u5bf9\u6570\u636e\uff0c\u5219\u4e0d\u4f1a\u8fdb\u884clikelihood\u8ba1\u7b97\uff0c\u867d\u7136\u80fd\u5f97\u5230mcmc\u6811\u4e14\u8ba1\u7b97\u901f\u5ea6\u98de\u5feb\uff0c\u4f46\u662f\u5176\u5206\u6b67\u65f6\u95f4\u7ed3\u679c\u662f\u6709\u95ee\u9898\u7684\uff1b1\uff0c\u8868\u793a\u4f7f\u7528\u591a\u5e8f\u5217\u6bd4\u5bf9\u6570\u636e\u8fdb\u884clikelihood\u8ba1\u7b97\uff0c\u6b63\u5e38\u8fdb\u884cMCMC\uff0c\u662f\u4e00\u822c\u4f7f\u7528\u7684\u53c2\u6570; 2\uff0c\u8fdb\u884c\u6b63\u5e38\u7684approximation likelihood\u5206\u6790\uff0c\u6b64\u65f6\u4e0d\u9700\u8981\u8bfb\u53d6\u591a\u5e8f\u5217\u6bd4\u5bf9\u6570\u636e\uff0c\u76f4\u63a5\u8bfb\u53d6\u5f53\u524d\u76ee\u5f55\u4e2d\u7684in.BV\u6587\u4ef6\u3002\u8be5\u6587\u4ef6\u662f\u4f7f\u7528usedata = 3\u53c2\u6570\u751f\u6210\u7684out.BV\u6587\u4ef6\u91cd\u547d\u540d\u800c\u6765\u7684\u3002\u6b64\u5916\uff0c\u7531\u4e8e\u7a0b\u5e8fBUG\uff0c\u5f53\u8bbe\u7f6eusedata = 2\u65f6\uff0c\u4e00\u5b9a\u8981\u5728\u6539\u884c\u53c2\u6570\u540e\u52a0 *\uff0c\u5426\u5219\u7a0b\u5e8f\u62a5\u9519 Error: file name empty.. 3\uff0c\u7a0b\u5e8f\u5229\u7528\u591a\u5e8f\u5217\u6bd4\u5bf9\u6570\u636e\u8c03\u7528baseml\/codeml\u547d\u4ee4\u5bf9\u6570\u636e\u8fdb\u884c\u5206\u6790\uff0c\u751f\u6210out.BV\u6587\u4ef6\u3002\u7531\u4e8emcmctree\u8c03\u7528baseml\/codeml\u8fdb\u884c\u8ba1\u7b97\u7684\u53c2\u6570\u8bbe\u7f6e\u53ef\u80fd\u4e0d\u592a\u597d\uff08\u7279\u522b\u65f6\u5bf9\u86cb\u767d\u5e8f\u5217\u8fdb\u884c\u8ba1\u7b97\u65f6\uff09\uff0c\u63a8\u8350\u81ea\u5df1\u4fee\u8be5\u8f6f\u4ef6\u81ea\u52a8\u751f\u6210\u7684baseml\/codeml\u914d\u7f6e\u6587\u4ef6\uff0c\u7136\u540e\u518d\u624b\u52a8\u8fd0\u884cbaseml\/codeml\u547d\u4ee4\uff0c\u518d\u6574\u5408\u5176\u7ed3\u679c\u6587\u4ef6\u4e3aout.BV\u6587\u4ef6\u3002\n   cleandata = 0         *\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       clock = 2         *\u8bbe\u7f6e\u5206\u5b50\u79cd\u65b9\u6cd5\uff1a1\uff0cglobal clock\u65b9\u6cd5\uff0c\u8868\u793a\u6240\u6709\u5206\u652f\u8fdb\u5316\u901f\u7387\u4e00\u81f4\uff1b2\uff0cindependent rates\u65b9\u6cd5\uff0c\u5404\u5206\u652f\u7684\u8fdb\u5316\u901f\u7387\u72ec\u7acb\u4e14\u8fdb\u5316\u901f\u7387\u7684\u5bf9\u6570log(r)\u7b26\u5408\u6b63\u6001\u5206\u5e03; 3\uff0ccorrelated rates\u65b9\u6cd5\uff0c\u548c\u65b9\u6cd52\u7c7b\u4f3c\uff0c\u4f46\u662flog(r)\u7684\u65b9\u5dee\u548c\u65f6\u95f4t\u76f8\u5173\u3002\n*    TipDate = 1 100     *\u5f53\u5916\u90e8\u8282\u70b9\u7531\u53d6\u6837\u65f6\u95f4\u65f6\u4f7f\u7528\u8be5\u53c2\u6570\u8fdb\u884c\u8bbe\u7f6e\uff0c\u540c\u65f6\u8be5\u53c2\u6570\u4e5f\u8bbe\u7f6e\u4e86\u65f6\u95f4\u5355\u4f4d\u3002\u5177\u4f53\u6570\u636e\u793a\u4f8b\u8bf7\u89c1examples\/TipData\u6587\u4ef6\u5939\u3002\n     RootAge = '<1.0'    *\u8bbe\u7f6eroot\u8282\u70b9\u7684\u5206\u6b67\u65f6\u95f4\uff0c\u4e00\u822c\u8bbe\u7f6e\u4e00\u4e2a\u6700\u5927\u503c\u3002\n \n*\u4f4d\u70b9\u66ff\u6362\u6a21\u578b\u53c2\u6570\uff1a<\/b>\n       model = 4         *\u8bbe\u7f6e\u78b1\u57fa\u66ff\u6362\u6a21\u578b\uff1a0\uff0cJC69\uff1b1\uff0cK80\uff1b2\uff0cF81\uff1b3\uff0cF84\uff1b4\uff0cHKY85\u3002\u5f53\u8bbe\u7f6eusedata = 1\u65f6\uff0c\u4e0d\u80fd\u4f7f\u7528\u5176\u5b83\u78b1\u57fa\u66ff\u6362\u6a21\u578b\u3002\u82e5\u9700\u8981\u9009\u62e9\u5176\u5b83\u78b1\u57fa\u66ff\u6362\u6a21\u578b\uff0c\u5219\u8003\u8651\u4f7f\u7528usedata = 3\u53c2\u6570\uff0c\u5c31\u53ef\u4ee5\u8bbe\u7f6emodel\u53c2\u6570\u503c\u4e3a\u5176\u5b83\u7684\u78b1\u57fa\u66ff\u6362\u6a21\u578b\u3002\u6b64\u65f6\uff0c\u7a0b\u5e8f\u4f1a\u5c06\u6570\u636e\u8fdb\u884c\u5206\u5272\uff0c\u4f8b\u5982\uff0cndata = 3\uff0c\u5219\u7a0b\u5e8f\u5206\u522b\u5bf93\u4e2a\u6570\u636e\u8fdb\u884c\u5206\u6790\uff0c\u751f\u6210baseml\u7684\u8f93\u5165\u6587\u4ef6\uff0c\u5e76\u8c03\u7528baseml\u8fdb\u884c\u5206\u6790\uff08\u82e5\u6570\u636e\u91cf\u8f83\u5927\uff0c\u5206\u6790\u8f83\u6162\uff0c\u63a8\u8350\u6309ctrl + c \u5f3a\u884c\u7ec8\u6b62\uff0c\u7a0b\u5e8f\u5219\u7ec8\u6b62baseml\u7684\u8fd0\u884c\uff0c\u8fdb\u884c\u4e0b\u4e00\u4e2a\u6570\u636e\u7684\u8f93\u5165\u6587\u4ef6\u751f\u6210\u5e76\u8fd0\u884c\u4e0b\u4e2a\u6570\u636e\u7684baseml\u547d\u4ee4\uff0c\u518d\u6309 ctrl + c \u5f3a\u884c\u7ec8\u6b62\uff0c\u8fd9\u6837\u53ef\u4ee5\u8ba9\u7a0b\u5e8f\u751f\u62103\u5404\u6570\u636e\u7684\u8f93\u5165\u6587\u4ef6\u548cbaseml\u914d\u7f6e\u6587\u4ef6\uff0c\u7136\u540e\u624b\u52a8\u5e76\u884c\u5316\u8fd0\u884c\uff0c\u52a0\u5feb\u65f6\u95f4\uff09\uff1b\u6bcf\u4e2a\u5206\u6790\u7ed3\u679c\u4e2d\u4f1a\u5f97\u5230rst2\u7ed3\u679c\u6587\u4ef6\uff1b\u53ef\u4ee5\u5728\u6b64\u5904\u624b\u52a8\u4fee\u6539tmp0001.ctl\u914d\u7f6e\u6587\u4ef6\uff0c\u4f8b\u5982\uff0c\u4fee\u6539\u5176model\u53c2\u6570\u503c\uff0c\u63a8\u8350\u4fee\u6539outfile\u53c2\u6570\u503c\uff0c\u4ece\u800c\u53ef\u4ee5\u624b\u52a8\u5e76\u884c\u5316\u8fd0\u884cbaseml\u547d\u4ee4\uff1b\u7136\u540e\u5c06\u6240\u6709\u6570\u636e\u7684rst2\u7ed3\u679c\u4f7f\u7528cat\u547d\u4ee4\u5408\u5e76\u6210\u6587\u4ef6in.BV\uff0c\u7528\u4e8e\u4e0b\u4e00\u6b65\u8bbe\u7f6e\u53c2\u6570usedata = 2\uff0c\u8fdb\u884cMCMC\u5206\u6790\u3002\n       alpha = 0.5       *\u6838\u9178\u5e8f\u5217\u4e2d\u4e0d\u540c\u4f4d\u70b9\uff0c\u5176\u8fdb\u5316\u901f\u7387\u4e0d\u4e00\u81f4\uff0c\u5176\u53d8\u5f02\u901f\u7387\u670d\u4eceGAMMA\u5206\u5e03\u3002\u4e00\u822c\u8bbe\u7f6eGAMMA\u5206\u5e03\u7684alpha\u503c\u4e3a0.5\u3002\u82e5\u8be5\u53c2\u6570\u503c\u8bbe\u7f6e\u4e3a0\uff0c\u5219\u8868\u793a\u6240\u6709\u4f4d\u70b9\u7684\u8fdb\u5316\u901f\u7387\u4e00\u81f4\u3002\u6b64\u5916\uff0c\u5f53userdata = 2\u65f6\uff0calpha\u3001ncatG\u3001alpha_gamma\u3001kappa_gamma\u8fd94\u4e2aGAMMA\u53c2\u6570\u65e0\u6548\u3002\u56e0\u4e3auserdata = 2\u65f6\uff0c\u4e0d\u4f1a\u5229\u7528\u5230\u591a\u5e8f\u5217\u6bd4\u5bf9\u7684\u6570\u636e\u3002\n       ncatG = 5         *\u8bbe\u7f6e\u79bb\u6563\u578bGAMMA\u5206\u5e03\u7684categories\u503c\u3002\n     BDparas = 1 1 0.1   *\u8bbe\u7f6e\u51fa\u751f\u7387\u3001\u6b7b\u4ea1\u7387\u548c\u53d6\u6837\u6bd4\u4f8b\u3002\u82e5\u8f93\u5165\u6709\u6839\u6811\u6587\u4ef6\u4e2d\u7684\u65f6\u95f4\u5355\u4f4d\u53d1\u751f\u6539\u53d8\uff0c\u5219\u9700\u8981\u76f8\u5e94\u4fee\u6539\u51fa\u751f\u7387\u548c\u6b7b\u4ea1\u7387\u7684\u503c\u3002\u4f8b\u5982\uff0c\u65f6\u95f4\u5355\u4f4d\u7531100Myr\u53d8\u6362\u4e3a1Myr\uff0c\u5219\u8981\u8bbe\u7f6e\u6210\".01 .01 0.1\"\u3002\n kappa_gamma = 6 2       *\u8bbe\u7f6ekappa\uff08\u8f6c\u6362\/\u98a0\u6362\u6bd4\u7387\uff09\u7684GAMMA\u5206\u5e03\u53c2\u6570\u3002\n alpha_gamma = 1 1       *\u8bbe\u7f6eGAMMA\u5f62\u72b6\u53c2\u6570alpha\u7684GAMMA\u5206\u5e03\u53c2\u6570\u3002 \n\n*\u8fdb\u5316\u901f\u7387\u53c2\u6570\uff1a<\/b>\n rgene_gamma = 2 20 1    *\u8bbe\u7f6e\u5e8f\u5217\u4e2d\u6240\u6240\u6709\u4f4d\u70b9\u5e73\u5747[\u78b1\u57fa\/\u5bc6\u7801\u5b50\/\u6c28\u57fa\u9178]\u66ff\u6362\u7387\u7684Dirichlet-GAMMA\u5206\u5e03\u53c2\u6570\uff1aalpha=2\u3001beta=20\u3001\u521d\u59cb\u5e73\u5747\u66ff\u6362\u7387\u4e3a\u6bcf100million\u5e74\uff08\u53d6\u51b3\u4e8e\u8f93\u5165\u6709\u6839\u6811\u6587\u4ef6\u4e2d\u7684\u65f6\u95f4\u5355\u4f4d\uff091\u4e2a\u66ff\u6362\u3002\u82e5\u65f6\u95f4\u5355\u4f4d\u7531100Myr\u53d8\u6362\u4e3a1Myr\uff0c\u5219\u8981\u8bbe\u7f6e\u6210\"2 2000 1\"\u3002\u603b\u4f53\u4e0a\u7684\u5e73\u5747\u8fdb\u5316\u901f\u7387\u4e3a\uff1a2 \/ 20 = 0.1 \u4e2a\u66ff\u6362 \/ \u6bcf100Myr\uff0c\u5373\u6bcf\u4e2a\u4f4d\u70b9\u6bcf\u5e74\u7684\u66ff\u6362\u6570\u4e3a 1e-9\u3002\nsigma2_gamma = 1 10 1    *\u8bbe\u7f6e\u6240\u6709\u4f4d\u70b9\u8fdb\u5316\u901f\u7387\u53d6\u5bf9\u6570\u540e\u65b9\u5dee\uff08sigma\u7684\u5e73\u65b9\uff09\u7684Dirichlet-GAMMA\u5206\u5e03\u53c2\u6570\uff1aalpha=1\u3001beta=10\u3001\u521d\u59cb\u65b9\u5dee\u503c\u4e3a1\u3002\u5f53clock\u53c2\u6570\u503c\u4e3a1\u65f6\uff0c\u8868\u793a\u4f7f\u7528\u5168\u5c40\u7684\u8fdb\u5316\u901f\u7387\uff0c\u5404\u5206\u679d\u7684\u8fdb\u5316\u901f\u7387\u6ca1\u6709\u5dee\u5f02\uff0c\u5373\u65b9\u5dee\u4e3a0\uff0c\u8be5\u53c2\u6570\u65e0\u6548\uff1b\u5f53clock\u53c2\u6570\u503c\u4e3a2\u65f6\uff0c\u82e5\u4fee\u6539\u4e86\u65f6\u95f4\u5355\u4f4d\uff0c\u8be5\u53c2\u6570\u503c\u4e0d\u9700\u8981\u6539\u53d8\uff1b\u5f53clock\u53c2\u6570\u503c\u4e3a3\u65f6\uff0c\u82e5\u4fee\u6539\u4e86\u65f6\u95f4\u5355\u4f4d\uff0c\u8be5\u53c2\u6570\u503c\u9700\u8981\u6539\u53d8\u3002\n    finetune = 1: .1 .1 .1 .1 .1 .1    *\u5192\u53f7\u524d\u7684\u503c\u8bbe\u7f6e\u662f\u5426\u81ea\u52a8\u8fdb\u884cfinetune\uff0c\u4e00\u822c\u8bbe\u7f6e\u62101\uff0c\u7136\u7a0b\u5e8f\u81ea\u52a8\u8fdb\u884c\u4f18\u5316\u5206\u6790\uff1b\u5192\u53f7\u540e\u9762\u8bbe\u7f6e\u5404\u4e2a\u53c2\u6570\u7684\u6b65\u8fdb\u503c\uff1atimes, musigma2, rates, mixing, paras, FossilErr\u3002\u7531\u4e8e\u6709\u4e86\u81ea\u52a8\u8bbe\u7f6e\uff0c\u8be5\u53c2\u6570\u4e0d\u50cf\u4ee5\u524d\u7248\u672c\u90a3\u4e48\u91cd\u8981\u4e86\uff0c\u53ef\u80fd\u4ee5\u540e\u4f1a\u53d6\u6d88\u8be5\u53c2\u6570\u3002\n\n*MCMC\u53c2\u6570\uff1a<\/b>\n       print = 1         *\u8bbe\u7f6e\u6253\u5370mcmc\u7684\u53d6\u6837\u4fe1\u606f\uff1a0\uff0c\u4e0d\u6253\u5370mcmc\u7ed3\u679c\uff1b1\uff0c\u6253\u5370\u9664\u4e86\u5206\u652f\u8fdb\u5316\u901f\u7387\u7684\u5176\u5b83\u4fe1\u606f\uff08\u5404\u5185\u90e8\u8282\u70b9\u5206\u6b67\u65f6\u95f4\u3001\u5e73\u5747\u8fdb\u5316\u901f\u7387\u3001sigma2\u503c\uff09\uff1b2\uff0c\u6253\u5370\u6240\u6709\u4fe1\u606f\u3002 \n      burnin = 2000      *\u5c06\u524d2000\u6b21\u8fed\u4ee3burnin\u540e\uff0c\u518d\u8fdb\u884c\u53d6\u6837\uff08\u5373\u6253\u5370\u51fa\u8be5\u6b21\u8fed\u4ee3\u8ba1\u7b97\u7684\u7ed3\u679c\u4fe1\u606f\uff0c\u5404\u5185\u90e8\u8282\u70b9\u5206\u6b67\u65f6\u95f4\u3001\u5e73\u5747\u8fdb\u5316\u901f\u7387\u3001sigma2\u503c\u548c\u5404\u5206\u652f\u8fdb\u5316\u901f\u7387\u7b49\uff09\u3002\n    sampfreq = 10        *\u6bcf10\u6b21\u8fed\u4ee3\u5219\u53d6\u6837\u4e00\u6b21\u3002\n     nsample = 20000     *\u5f53\u53d6\u6837\u6b21\u6570\u8fbe\u5230\u8be5\u6b21\u6570\u65f6\uff0c\u5219\u53d6\u6837\u7ed3\u675f\uff08\u7a0b\u5e8f\u4e5f\u5c06\u8fd0\u884c\u7ed3\u675f\uff09\u3002\n<\/pre>\n\n\n\n
a4. \u8fd0\u884cmcmctree\u547d\u4ee4\u4f7f\u7528\u8fdb\u884c\u5206\u6b67\u65f6\u95f4\u8ba1\u7b97<\/h2>\n\n\n\n
\u7a0b\u5e8f\u8fd0\u884c\u547d\u4ee4\uff1a<\/p>\n\n\n\n
mcmctree mcmctree.ctl<\/code><\/pre>\n\n\n\n
5. \u7ed3\u679c\u6587\u4ef6\u89e3\u91ca<\/h2>\n\n\n\n
\u7a0b\u5e8f\u5728\u8fd0\u884c\u8fc7\u7a0b\u4e2d\uff0c\u4f1a\u5728\u5c4f\u5e55\u751f\u751f\u6210\u4e00\u4e9b\u4fe1\u606f\u3002\u6bd4\u8f83\u8017\u65f6\u95f4\u7684\u6b65\u9aa4\u4e3b\u8981\u5728\u4e8e\u53d6\u6837\u7684\u767e\u5206\u6bd4\u8fdb\u5ea6\uff1a<\/p>\n\n\n\n
\u7b2c\u4e00\u5217\uff1a\u53d6\u6837\u7684\u767e\u5206\u6bd4\u8fdb\u5ea6\u3002
\u7b2c2~6\u5217\uff1a\u53c2\u6570\u7684\u63a5\u53d7\u6bd4\u4f8b\u3002\u4e00\u822c\uff0c\u5176\u503c\u5e94\u8be5\u572830%\u5de6\u53f3\u300220~40%\u662f\u5f88\u597d\u7684\u7ed3\u679c\uff0c15~70%\u662f\u53ef\u4ee5\u63a5\u53d7\u7684\u8303\u56f4\u3002\u82e5\u8fd9\u4e9b\u503c\u5728\u5f00\u59cb\u65f6\u53d8\u52a8\u8f83\u5927\uff0c\u5219\u8868\u793aburnin\u6570\u8bbe\u7f6e\u592a\u5c0f\u3002
\u7b2c7~x\u5217\uff1a\u5404\u5185\u90e8\u8282\u70b9\u7684\u5e73\u5747\u5206\u6b67\u65f6\u95f4\uff0c\u7b2c7\u5217\u5219\u662froot\u8282\u70b9\u7684\u5e73\u5747\u5206\u6b67\u65f6\u95f4\u3002\u82e5\u6709y\u4e2a\u7269\u79cd\uff0c\u5219\u603b\u5171\u6709y-1\u4e2a\u5185\u90e8\u8282\u70b9\uff0c\u4ece\u7b2c7\u5217\u5f00\u59cb\u540e\u7684y-1\u5217\u5bf9\u5e94\u8fd9\u4e9b\u5185\u90e8\u8282\u70b9\u3002
\u5012\u6570\u7b2c3~x\u5217\uff1ar_left\u503c\u3002\u82e5\u8f93\u51653\u5404\u591a\u5e8f\u5217\u6bd4\u5bf9\u7ed3\u679c\uff0c\u5219\u67093\u5217\u3002x\u5217\u7684\u524d\u4e00\u5217\u662f\u4e2d\u5212\u7ebf - \u3002
\u5012\u6570\u7b2c1~2\u5217\uff1alikelihood\u503c\u548c\u65f6\u95f4\u6d88\u8017\u3002
<\/pre>\n\n\n\n
\u5c4f\u5e55\u4fe1\u606f\u6700\u540e\uff0c\u7ed9\u51fa\u5404\u4e2a\u5185\u90e8\u8282\u70b9\u7684\u5206\u6b67\u65f6\u95f4(t)\u3001\u5e73\u5747\u53d8\u5f02\u901f\u7387(mu)\u3001\u53d8\u5f02\u901f\u7387\u65b9\u5dee(sigma2)\u548cr_left\u7684Posterior\u4fe1\u606f\uff1a\u5747\u503c(mean)\u300195%\u53cc\u4fa7\u7f6e\u4fe1\u533a\u95f4(95% Equal-tail CI)\u548c95% HPD\u7f6e\u4fe1\u533a\u95f4(95% HPD CI)\u7b49\u4fe1\u606f\u3002\u6b64\u5916\uff0c\u5012\u6570\u7b2c\u4e8c\u5217\u7ed9\u51fa\u4e86\u5404\u4e2a\u5185\u90e8\u8282\u70b9\u7684Posterior mean time\u4fe1\u606f\uff0c\u53ef\u4ee5\u7528\u4e8e\u6536\u655b\u5206\u6790\u3002<\/p>\n\n\n\n
\u5728\u5f53\u524d\u76ee\u5f55\u4e0b\uff0c\u751f\u6210\u51e0\u4e2a\u4e3b\u8981\u7ed3\u679c\uff1a<\/p>\n\n\n\n
FigTree.tre    \u751f\u6210\u542b\u6709\u5206\u6b67\u65f6\u95f4\u7684\u8d85\u5ea6\u91cf\u6811\u6587\u4ef6
mcmc.txt       MCMC\u53d6\u6837\u4fe1\u606f\uff0c\u5305\u542b\u5404\u5185\u90e8\u8282\u70b9\u5206\u6b67\u65f6\u95f4\u3001\u5e73\u5747\u8fdb\u5316\u901f\u7387\u3001sigma2\u503c\u7b49\u4fe1\u606f\uff0c\u53ef\u4ee5\u5728Tracer\u8f6f\u4ef6\u4e2d\u6253\u5f00\u3002\u901a\u8fc7\u67e5\u770b\u5404\u53c2\u6570\u7684ESS\u503c\uff0c\u82e5ESS\u503c\u5927\u4e8e200\uff0c\u5219\u4ece\u4e00\u5b9a\u7a0b\u5ea6\u4e0a\u8868\u793aMCMC\u8fc7\u7a0b\u80fd\u6536\u655b\uff0c\u7ed3\u679c\u53ef\u9760\u3002<\/code>
out.txt        \u5305\u542b\u7531\u8f83\u591a\u4fe1\u606f\u7684\u7ed3\u679c\u6587\u4ef6\u3002\u4f8b\u5982\uff0c\u5404\u78b1\u57fa\u9891\u7387\u3001\u8282\u70b9\u547d\u540d\u4fe1\u606f\u3001\u5404\u8282\u70b9\u5206\u6b67\u65f6\u95f4\u3001\u8fdb\u5316\u901f\u7387\u548c\u8fdb\u5316\u6811\u7b49\u3002<\/pre>\n\n\n\n
6. \u4f7f\u7528approximate likelihood\u65b9\u6cd5\u66f4\u5feb\u901f\u5730\u8ba1\u7b97\u5206\u6b67\u65f6\u95f4<\/h2>\n\n\n\n
\u6309\u7167\u4ee5\u4e0a\u65b9\u6cd5\u8fdb\u884cMCMC\u8ba1\u7b97\u975e\u5e38\u6d88\u8017\u8ba1\u7b97\u3002\u4e3a\u4e86\u52a0\u5feb\u8ba1\u7b97\u901f\u5ea6\uff0c\u53ef\u4ee5\u5c06\u5206\u6790\u5206\u6210\u4e24\u4e2a\u6b65\u9aa4\uff1a\uff081\uff09\u9996\u5148\uff0c\u4f7f\u7528Maximum Likelihood\u65b9\u6cd5\u8ba1\u7b97\u679d\u957f\u548cHessian\u4fe1\u606f\uff1b\uff082\uff09\u518d\u4f7f\u7528MCMC\u65b9\u6cd5\u8ba1\u7b97\u5206\u6b67\u65f6\u95f4\u3002<\/p>\n\n\n\n
\u8fd0\u884c\u6b65\u9aa4\u4e5f\u76f8\u5e94\u5206\u6210\u4e24\u6b65\uff1a\uff081\uff09\u8bbe\u7f6e\u914d\u7f6e\u6587\u4ef6\u4e2d\u53c2\u6570 usedata = 3\uff0c\u7136\u540e\u548c\u4e0a\u9762\u540c\u6837\u8fd0\u884cmcmctree\u547d\u4ee4\uff0c\u8f6f\u4ef6\u4f1a\u5bf9\u5404\u4e2a\u591a\u5e8f\u5217\u6bd4\u5bf9\u7ed3\u679c\u8c03\u7528baseml\/codeml\u547d\u4ee4\u8fdb\u884c\u5206\u6b67\u65f6\u95f4\u8ba1\u7b97\uff0c\u751f\u6210\u7ed3\u679c\u6587\u4ef6rst2\uff0c\u5c06\u5404\u4e2a\u591a\u5e8f\u5217\u6bd4\u5bf9\u7ed3\u679c\u6587\u4ef6\u5185\u5bb9\u76f4\u63a5cat\uff08linux\u7cfb\u7edf\u7684\u5e38\u7528\u547d\u4ee4\uff09\u5408\u5e76\u6210out.BV\u6587\u4ef6\uff1b\uff082\uff09\u7136\u540e\u5c06out.BV\u6587\u4ef6\u91cd\u547d\u540d\u4e3ain.BV\uff0c\u5e76\u5c06\u914d\u7f6e\u6587\u4ef6\u4e2d\u53c2\u6570 usedata = 2\uff0c\u518d\u6b21\u8fd0\u884c\u540c\u6837\u7684mcmctree\u547d\u4ee4\uff0c\u7a0b\u5e8f\u4f1a\u8fd0\u884cMCMC\u5206\u6790\u5e76\u5f97\u5230\u7ed3\u679c\u3002\u4f7f\u7528\u8be5\u65b9\u6cd5\uff0c\u5176MCMC\u901f\u5ea6\u5feb\u5f88\u591a\u3002<\/p>\n\n\n\n
\u82e5\u8f93\u5165\u6570\u636e\u662fprotein\u5e8f\u5217\uff0c\u5219mcmctree\u8c03\u7528codeml\u547d\u4ee4\u8fdb\u884c\u5206\u6790\u65f6\u7684model\u53c2\u6570\u9009\u62e9\u662f\u4e0d\u6b63\u786e\u7684\uff0c\u9700\u8981\u81ea\u5df1\u624b\u52a8\u4fee\u6539codeml\u547d\u4ee4\u7684\u53c2\u6570\u914d\u7f6e\u6587\u4ef6\u540e\u518d\u8fd0\u884ccodeml\u547d\u4ee4\uff0c\u5e76\u5c06\u5176\u7ed3\u679c\u6587\u4ef6rst2\u7684\u5185\u5bb9\u5408\u5e76\u5230out.BV\u6587\u4ef6\u4e2d\u3002\u82e5\u60f3\u4f7f\u7528\u66f4\u590d\u6742\u7684\u6a21\u578b\uff0c\u5982GTR\u8fdb\u884cmcmctree\u5206\u6790\uff0c\u5219\u6309\u540c\u6837\u65b9\u6cd5\u624b\u52a8\u4fee\u6539\u914d\u7f6e\u6587\u4ef6\u5e76\u5141\u8bb8baseml\u547d\u4ee4\uff0c\u6700\u540e\u5c06rst2\u7684\u5185\u5bb9\u6574\u5408\u5230out.BV\u6587\u4ef6\u4e2d\u3002\u6b64\u5916\uff0c\u53ef\u4ee5\u5c06\u5206\u522b\u6765\u81ea\u6838\u9178(\u975e\u7f16\u7801RNA)\u548c\u86cb\u767d\u7684rst2\u5185\u5bb9\u540c\u65f6\u6574\u5408\u5230out.BV\u4e2d\u8fdb\u884c\u8ba1\u7b97\u3002<\/p>\n\n\n\n
7. \u4f7f\u7528infinitesites\u8f93\u5165\u542b\u6709\u679d\u957f\u4fe1\u606f\u7684\u7cfb\u7edf\u8fdb\u5316\u6811\u5feb\u901f\u8fdb\u884c\u5206\u6b67\u65f6\u95f4\u8ba1\u7b97<\/h2>\n\n\n\n
infinitesites\u7a0b\u5e8f\u8fdb\u884c\u5206\u6b67\u65f6\u95f4\u8ba1\u7b97\u65f6\uff0c\u5176\u5047\u8bbe\u524d\u63d0\u4e3a\u591a\u5e8f\u5217\u6bd4\u5bf9\u7684\u5e8f\u5217\u957f\u5ea6\u4e3a\u65e0\u9650\u957f\u3002\u76f8\u6bd4\u4e8e\u6b63\u5e38\u7684mcmctree\u547d\u4ee4\uff0c\u8981\u6c42\u989d\u5916\u591a\u8f93\u5165\u4e00\u4e2a\u540d\u4e3a FixedDsClock23.txt \u7684\u6587\u4ef6\u3002\u8be5\u6587\u4ef6\u4e2d\u5b58\u653e\u4e86\u76f8\u5e94\u7684\u5e26\u6709\u679d\u957f\u4fe1\u606f\u7684\u7cfb\u7edf\u53d1\u80b2\u6811\u3002\u8be5\u6587\u4ef6\u4e2d\u7cfb\u7edf\u53d1\u80b2\u6811\u7684\u62d3\u6251\u7ed3\u6784\u8981\u548cinput.trees\u4e00\u81f4\u3002\u63a8\u8350\u4f7f\u7528baseml\u547d\u4ee4\u8f93\u5165input.trees\u548c\u591a\u5e8f\u5217\u6bd4\u5bf9\u7ed3\u679c\u8ba1\u7b97\u679d\u957f\u3002<\/p>\n\n\n\n
FixedDsClock23.txt \u6587\u4ef6\u5185\u5bb9\u793a\u4f8b\uff1a<\/p>\n\n\n\n
7
((((human: 0.029043, (chimpanzee: 0.014557, bonobo: 0.010908): 0.016729): 0.015344, gorilla: 0.033888): 0.033816, (orangutan: 0.026872, sumatran: 0.022437): 0.069648): 0.073309, gibbon: 0.024637);
((((human: 0.012463, (chimpanzee: 0.002782, bonobo: 0.003835): 0.003331): 0.004490, gorilla: 0.014278): 0.006308, (orangutan: 0.010818, sumatran: 0.008845): 0.030551): 0.004363, gibbon: 0.029246);
((((human: 0.270862, (chimpanzee: 0.066698, bonobo: 0.056883): 0.124104): 0.139082, gorilla: 0.310797): 0.391342, (orangutan: 0.152555, sumatran: 0.114176): 0.696518): 0.017607, gibbon: 1.394718);<\/pre>\n\n\n\n
\u8fd0\u884cinfinitesites\u547d\u4ee4\u8fdb\u884c\u5206\u6b67\u65f6\u95f4\u8ba1\u7b97\uff1a<\/p>\n\n\n\n
infinitesites mcmctree.ctl<\/code><\/pre>\n\n\n\n
\u4f7f\u7528infinitesites\u8fdb\u884c\u5206\u6b67\u65f6\u95f4\u8ba1\u7b97\u65f6\uff0c\u7a0b\u5e8f\u8981\u6c42\u8f93\u5165\u591a\u5e8f\u5217\u6bd4\u5bf9\u6587\u4ef6\u3002\u867d\u7136\u7a0b\u5e8f\u8bfb\u53d6\u4e86\u5e8f\u5217\u4fe1\u606f\uff0c\u4f46\u5728\u8ba1\u7b97\u65f6\u4f1a\u5ffd\u7565\u5176\u5e8f\u5217\u4fe1\u606f\u3002<\/p>\n\n\n\n
8. \u4e00\u4e9b\u5176\u5b83\u6ce8\u610f\u4e8b\u9879<\/h2>\n\n\n\n
(1) \u5982\u4f55\u68c0\u6d4bMCMC\u7684\u7ed3\u679c\u662f\u5426\u8fbe\u5230\u6536\u655b\u72b6\u6001\uff1f<\/p>\n\n\n\n
\u6536\u655b\u7684\u610f\u601d\uff0c\u5373\u7ecf\u8fc7\u5f88\u591a\u6b21\u8fed\u4ee3\u540e\uff0c\u5f97\u5230\u7684MCMC\u6811\u7684\u5404\u679d\u957f\u8d8b\u4e8e\u4e00\u4e2a\u5b9a\u503c\uff0c\u53d8\u52a8\u975e\u5e38\u5c0f\u3002\u4e8e\u662f\uff0c\u6700\u76f4\u63a5\u7684\u68c0\u6d4b\u65b9\u6cd5\u662f\uff1a\u5206\u522b\u4f7f\u7528\u4e0d\u540c\u7684Seed\u503c\u8fdb\u884cmcmctree\u6216infinitesites\u8fdb\u884c\u4e24\u6b21\u6216\u591a\u6b21\u5206\u6790\uff0c\u7136\u540e\u6bd4\u8f83\u4e24\u4e2a\u7ed3\u679c\u6811\u662f\u5426\u4e00\u81f4\uff0c\u5b9e\u9645\u5c31\u662f\u6bd4\u8f83\u6811\u6587\u4ef6\u4e2d\u5404\u5185\u90e8\u8282\u70b9\u7684Height\u503c\uff08\u5206\u6b67\u65f6\u95f4 \/ Posterior time\uff09\u3002\u6bd4\u8f83\u65b9\u6cd5\u53ef\u4ee5\u6709\u591a\u79cd: (a) \u7ed3\u679c\u6587\u4ef6mcmc.txt\u4e2d\u6bcf\u884c\u8bb0\u5f55\u4e86\u4e00\u4e2a\u53d6\u6837\u7684\u7ed3\u679c\uff0c\u5305\u542b\u5404\u5185\u90e8\u8282\u70b9\u7684Posterior time\u503c\uff0c\u5373\u8fdb\u5316\u6811\u7684Height\u503c\uff0c\u5bf9\u8be5mcmc.txt\u6587\u4ef6\u8fdb\u884c\u5206\u6790\uff0c\u5f97\u5230\u6bcf\u4e2a\u5185\u90e8\u8282\u70b9\u7684Posterior mean time\u503c\u3002\u7136\u540e\u4f5c\u56fe \uff08\u5b98\u65b9\u8bf4\u660e\u6587\u6863\u7b2c6\u9875\u56fe\u793a\uff09\uff0c\u6a2a\u5750\u6807\u8868\u793a\u7b2c\u4e00\u6b21\u8fd0\u884c\u7684\u5404\u5185\u90e8\u8282\u70b9\u7684\u5206\u6b67\u65f6\u95f4\u5747\u503c\u3001\u7eb5\u5750\u6807\u8868\u793a\u7b2c\u4e8c\u6b21\u8fd0\u884c\u7684\u5404\u5185\u90e8\u8282\u70b9\u7684\u5206\u6b67\u65f6\u95f4\u5747\u503c\u3002\u8be5\u6563\u70b9\u56fe\u8981\u8868\u73b0\u51fa\u975e\u5e38\u660e\u663e\u7684\u5bf9\u89d2\u7ebf\uff0c\u624d\u8ba4\u4e3a\u8fbe\u5230\u6536\u655b\u3002\u8fd9\u65f6\u53ef\u4ee5\u8003\u8651\u8ba1\u7b97\u5176\u76f8\u5173\u7cfb\u6570\u6765\u5224\u65ad\u662f\u5426\u7b26\u5408\u7ebf\u6027\u3002(b) \u6211\u89c9\u5f97\u7b2c\u4e00\u79cd\u5b98\u65b9\u6587\u6863\u7ed9\u7684\u65b9\u6cd5\u6bd4\u8f83\u9ebb\u70e6\u4e14\u662f\u5426\u7b26\u5408\u5bf9\u89d2\u7ebf\u6ca1\u6709\u660e\u786e\u7684\u5b9a\u4e49\uff0c\u4e8e\u662f\u5c31\u76f4\u63a5\u6bd4\u8f83\u4e24\u6b21\u7ed3\u679c\u6811\u6587\u4ef6\u4e2d\u7684\u5404\u679d\u957f\u3002\u8ba1\u7b97\u5404\u679d\u957f\u603b\u7684\u504f\u5dee\u767e\u5206\u6bd4\uff0c\u5f53\u504f\u5dee\u767e\u5206\u6bd4\u4f4e\u4e8e0.1%\uff0c\u5219\u8ba4\u4e3a\u4e24\u6b21\u7ed3\u679c\u975e\u5e38\u543b\u5408\uff0c\u5dee\u5f02\u4f4e\u4e8e0.1%\uff0c\u8ba4\u4e3a\u8fbe\u5230\u6536\u655b\u3002(c) \u6b64\u5916\uff0c\u8fd8\u53ef\u4ee5\u4f7f\u7528Tracer\u5206\u6790mcmc.txt\u6587\u4ef6\uff0c\u68c0\u6d4b\u5176ESS\u503c\uff0c\u4e00\u822c\u8ba4\u4e3a\u8be5\u503c\u9ad8\u4e8e200\uff0c\u5219\u53ef\u80fd\u8fbe\u5230\u6536\u655b\u3002\u8be5\u65b9\u6cd5\u53ef\u7528\u4e8e\u8f85\u52a9\u68c0\u6d4b\u3002\u6700\u540e\uff0c\u82e5\u4e0d\u6536\u655b\uff0c\u5219\u9700\u8981\u63d0\u9ad8burnin\u3001nsample\u503c\uff0c\u91cd\u65b0\u8fd0\u884c\u7a0b\u5e8f\u3002<\/p>\n\n\n\n
(2) \u5982\u4f55\u8bbe\u7f6eburnin\u3001sampfreq\u548cnsample\u503c\uff1f<\/p>\n\n\n\n
(a) \u4e00\u822c\u63a8\u8350\u8bbe\u7f6ensample\u503c\u4e0d\u5c0f\u4e8e20k(\u5b98\u65b9\u793a\u4f8b\u6570\u636e\u4e2d\u8bbe\u7f6e\u7684\u503c)\uff0c\u53ea\u6709\u5f53\u8be5\u503c\u8f83\u5927\u65f6\uff0c\u6c42\u5f97\u7684\u5747\u503c\u624d\u6709\u610f\u4e49\u3002(b) sampfreq\u8868\u793a\u53d6\u6837\u95f4\u9694\uff0c\u4e00\u822c\u8bbe\u7f6e\u4e3a10\uff0c100\u62161000\u3002nsample \u548csampfreq \u7684\u4e58\u79ef\u8868\u793a\u6709\u6548\u8fed\u4ee3\u7684\u6b21\u6570\uff0c\u8fd9\u4e9b\u8fed\u4ee3\u8d8a\u51c6\u786e\uff0c\u6b21\u6570\u8d8a\u5927\uff0c\u5219\u7ed3\u679c\u8d8a\u597d\uff0c\u8d8a\u8d8b\u4e8e\u6536\u655b\u3002\u5f53\u7136\uff0c\u6b21\u6570\u8d8a\u5927\uff0c\u8d8a\u6d88\u8017\u65f6\u95f4\u3002\u82e5\u6570\u636e\u91cf\u5f88\u5c0f\uff0c\u53ef\u4ee5\u8003\u8651\u8bbe\u7f6esampfreq\u4e3a1000\uff1b\u82e5\u6570\u636e\u91cf\u5927\uff0c\u6bcf\u6b21\u8fed\u4ee3\u8017\u65f6\u591a\uff0c\u5219\u8003\u8651\u8bbe\u7f6esampfre\u4e3a10\u3002(c) \u4e00\u822c\u6700\u5f00\u59cb\u7684\u8fed\u4ee3\u7ed3\u679c\u5f88\u5dee\uff0c\u9700\u8981\u53bb\u9664(burnin)\u5176\u7ed3\u679c\uff0c\u5219\u8bbe\u7f6eburnin\u503c\u3002\u8981\u8bbe\u7f6e\u8db3\u591f\u5927\u7684burnin\u503c\uff0c\u4fdd\u8bc1\u5728\u7a0b\u5e8f\u8fd0\u884c\u65f6\u5f53\u8fed\u4ee3\u6bd4\u4f8b\u8fbe\u52300% (\u5373burnin\u7ed3\u675f) \u65f6\uff0c\u5176\u53c2\u6570\u7684\u63a5\u53d7\u6bd4\u4f8b\u503c\u8f83\u597d\uff0c\u572830%\u5de6\u53f3\u4e14\u968f\u8fed\u4ee3\u6b21\u6570\u589e\u591a\u65f6\u53d8\u52a8\u5e45\u5ea6\u4e0d\u5927\u3002\u63a8\u8350\u8bbe\u7f6eburnin\u7684\u8fed\u4ee3\u6b21\u6570\u4e3a\u6709\u6548\u6b21\u6570\u768410~40%\u3002PAML\u8f6f\u4ef6\u65f6\u5148burnin\u540e\u518d\u8bb0\u5f55\u6709\u6548\u8fed\u4ee3\u7684\u53c2\u6570\u503c\uff1b\u5176\u5b83\u8f6f\u4ef6\u5982BEAST\u5219\u8bb0\u5f55\u6240\u6709\u7684\u53c2\u6570\u503c\u540e\uff0c\u6700\u540e\u6c47\u603b\u65f6burnin\u6389\u4e00\u5b9a\u6bd4\u4f8b\u7684\u6570\u636e\u3002(d) \u603b\u4f53\u4e0a\uff0c\u5176\u5b9e\u5c31\u662f\u4e24\u4e2a\u53c2\u6570\uff1aburnin\u6389\u7684\u8fed\u4ee3\u6b21\u6570\u548c\u7528\u4e8e\u8ba1\u7b97\u7ed3\u679c\u7684\u6709\u6548\u8fed\u4ee3\u6b21\u6570\u3002\u7531\u4e8e\u9700\u8981\u6839\u636e\u6709\u6548\u8fed\u4ee3\u6570\u636e\u6765\u8fdb\u884c\u5747\u503c\u8ba1\u7b97\uff0c\u82e5\u8bb0\u5f55\u6bcf\u6b21\u8fed\u4ee3\u7684\u53c2\u6570\uff0c\u5219\u751f\u6210\u7684mcmc.txt\u6587\u4ef6\u884c\u6570\u8fc7\u591a\uff0c\u6587\u4ef6\u592a\u5927\uff0c\u6c47\u603b\u65f6\u4e5f\u6d88\u8017\u8ba1\u7b97\u3002\u4e8e\u662f\u8bbe\u7f6e\u6ca1\u9694\u4e00\u5b9a\u8fed\u4ee3\u8f6e\u6570\u53d6\u6837\u4e00\u6b21\uff0c\u8fd9\u6837\u751f\u6210\u7684mcmc.txt\u6587\u4ef6\u4e0d\u4f1a\u592a\u5927\uff0c\u5bf9\u6700\u540e\u7684\u5747\u503c\u8ba1\u7b97\u5f71\u54cd\u4e0d\u5927\u3002(e) \u6211\u4e2a\u4eba\u63a8\u8350\u6709\u6548\u8fed\u4ee3\u6b21\u6570 1~10M \u6b21\uff0cburnin 0.2~4M\u6b21\u3002\u6309\u65f6\u95f4\u6d88\u8017\u4ece\u5c11\u5230\u591a\u7684\u53c2\u6570\u503c\uff1a<\/p>\n\n\n\n
\u6570\u636e\u7b80\u5355\u65f6\uff0c\u8fdb\u884c0.5M\u8fed\u4ee3\u6b21\u6570\uff0cburnin\u6bd4\u4f8b40%\uff1a{ burnin 200k; sampfreq 10; nsample 50k } 
\u6570\u636e\u4e2d\u7b49\u65f6\uff0c\u8fdb\u884c1M\u8fed\u4ee3\u6b21\u6570\uff0cburnin\u6bd4\u4f8b40%\uff1a{ burnin 400k; sampfreq 10; nsample 100k } 
\u6570\u636e\u590d\u6742\u65f6\uff0c\u8fdb\u884c5M\u8fed\u4ee3\u6b21\u6570\uff0cburnin\u6bd4\u4f8b20%\uff1a{ burnin 1000k; sampfreq 10; nsample 500k }
\u6570\u636e\u5de8\u5927\u65f6\uff0c\u8fdb\u884c10M\u8fed\u4ee3\u6b21\u6570\uff0cburnin\u6bd4\u4f8b20%\uff1a{ burnin 2000k; sampfreq 100; nsample 100k }

\u4f7f\u7528\u76f8\u5e94\u53c2\u6570\u8fdb\u884c\u5206\u6790\u540e\uff0c\u82e5\u4e0d\u6ee1\u610f\u5176\u6536\u655b\u7a0b\u5ea6\uff0c\u5219\u9009\u7528\u66f4\u591a\u8fed\u4ee3\u6b21\u6570\u7684\u53c2\u6570\u3002<\/pre>\n\n\n\n
<\/p>\n","protected":false},"excerpt":{"rendered":"
PAML\u8f6f\u4ef6\u4e2d\u7684mcmctree\u547d\u4ee4\u53ef\u4ee5\u4f7f\u7528Bayesian\u65b9\u6cd5\u4f30\u7b97\u7269\u79cd\u5206\u6b67\u65f6\u95f4 … \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":[1],"tags":[],"_links":{"self":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2974"}],"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=2974"}],"version-history":[{"count":33,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2974\/revisions"}],"predecessor-version":[{"id":3068,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2974\/revisions\/3068"}],"wp:attachment":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=2974"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=2974"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=2974"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}