{"id":3001,"date":"2019-10-23T17:51:45","date_gmt":"2019-10-23T09:51:45","guid":{"rendered":"http:\/\/www.chenlianfu.com\/?p=3001"},"modified":"2019-10-25T16:48:10","modified_gmt":"2019-10-25T08:48:10","slug":"%e4%bd%bf%e7%94%a8paml%e8%bd%af%e4%bb%b6%e5%88%a9%e7%94%a8%e6%a0%b8%e9%85%b8%e5%ba%8f%e5%88%97%e8%bf%9b%e8%a1%8c%e7%b3%bb%e7%bb%9f%e5%8f%91%e8%82%b2%e5%8f%82%e6%95%b0%e5%88%86%e6%9e%90","status":"publish","type":"post","link":"http:\/\/www.chenlianfu.com\/?p=3001","title":{"rendered":"\u4f7f\u7528PAML\u8f6f\u4ef6\u5229\u7528\u6838\u9178\u5e8f\u5217\u8fdb\u884c\u7cfb\u7edf\u53d1\u80b2\u53c2\u6570\u5206\u6790"},"content":{"rendered":"\n<p>PAML\u8f6f\u4ef6\u4e2d\u7684baseml\u547d\u4ee4\u53ef\u4ee5\u5229\u7528Maxmum Likelihood\u65b9\u6cd5\u8ba1\u7b97\u7cfb\u7edf\u53d1\u80b2\u4e2d\u7684\u76f8\u5173\u53c2\u6570\u3002basml\u547d\u4ee4\u80fd\u4ee5\u5206\u652f\u6811\u62d3\u6251\u7ed3\u6784\u4fe1\u606f\u548c\u591a\u5e8f\u5217\u6bd4\u5bf9\u4fe1\u606f\u4f5c\u4e3a\u8f93\u5165\uff0c\u5728\u53c2\u6570\u914d\u7f6e\u6587\u4ef6\u4e2d\u8bbe\u7f6e\u4e00\u4e9b\u63a7\u5236\u7a0b\u5e8f\u8fd0\u884c\u7684\u53c2\u6570\uff0c\u6765\u5bf9\u4e00\u4e9b\u8fdb\u5316\u8fc7\u7a0b\u4e2d\u7684\u53c2\u6570\u8fdb\u884c\u5206\u6790\u3002\u8fd9\u4e9b\u53c2\u6570\u4e3b\u8981\u6709\uff1a<\/p>\n\n\n\n<pre class=\"wp-block-preformatted\">1. \u5e8f\u5217\u4e2d\u5404\u78b1\u57fa\u9891\u7387\u3002<br>2. \u4e24\u4e24\u7269\u79cd\u4e4b\u95f4\u7684\u8ddd\u79bb\u3002<br>3. \u7cfb\u7edf\u53d1\u80b2\u6811\u7684\u679d\u957f\u4fe1\u606f\u3002<br>4. \u78b1\u57fa\u66ff\u6362\u77e9\u9635\u3002<br><\/pre>\n\n\n\n<p>PAML\u8f6f\u4ef6\u7684baseml\u793a\u4f8b\u6570\u636e\u4f4d\u4e8e\u8f6f\u4ef6\u5b89\u88c5\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 input.trees<\/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\u3002\u4f8b\u5982\uff1a<\/p>\n\n\n\n<pre class=\"wp-block-preformatted\">5  1<br>(((Human:0.1, Chimpanzee:0.2):0.8, Gorilla:0.3):0.7, Orangutan:0.4, Gibbon:0.5);<\/pre>\n\n\n\n<p>\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 <\/p>\n\n\n\n<h2>2. \u8f93\u5165\u6587\u4ef6\uff082\/3\uff09\uff1a\u6838\u9178\u5e8f\u5217\u6bd4\u5bf9\u7ed3\u679c input.txt<\/h2>\n\n\n\n<pre class=\"wp-block-preformatted\">5   895<br><br>Human       AAGCTTCACCGGCGCAGTCATTCTCATAATCGCCCACGGACTT...<br>Chimpanzee  AAGCTTCACCGGCGCAATTATCCTCATAATCGCCCACGGACTT...<br>Gorilla     AAGCTTCACCGGCGCAGTTGTTCTTATAATTGCCCACGGACTT...<br>Orangutan   AAGCTTCACCGGCGCAACCACCCTCATGATTGCCCATGGACTC...<br>Gibbon      AAGCTTTACAGGTGCAACCGTCCTCATAATCGCCCACGGACTA...<br><\/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\uff1abaseml\u547d\u4ee4\u7684\u914d\u7f6e\u6587\u4ef6baseml.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   *\u8f93\u5165\u6838\u9178\u591a\u5e8f\u5217\u6bd4\u5bf9\u7ed3\u679c\u6587\u4ef6\u8def\u5f84\n     treefile = input.trees *\u8f93\u5165\u7cfb\u7edf\u53d1\u80b2\u6811\u6587\u4ef6\u8def\u5f84\n      outfile = mlb         *\u8bbe\u7f6e\u8f93\u51fa\u6587\u4ef6\u8def\u5f84\n        noisy = 2           *\u8bbe\u7f6e\u5c4f\u5e55\u4e0a\u8f93\u51fa\u4fe1\u606f\u6a21\u5f0f\uff0c\u503c\u8d8a\u5927\u5219\u8f93\u51fa\u8d8a\u591a\u4fe1\u606f\uff1a0\uff0c1\uff0c2\uff0c3\u3002\n      verbose = 0           *\u7ed3\u679c\u6587\u4ef6\u4e2d\u7684\u8f93\u51fa\u4fe1\u606f\u65b9\u5f0f\uff1a1\uff0c\u8f93\u51fa\u8be6\u7ec6\u4fe1\u606f\uff0c\u5305\u542b\u78b1\u57fa\u5e8f\u5217\uff1b0\uff0c\u7cbe\u7b80\u6a21\u5f0f\u7ed3\u679c\uff08\u63a8\u8350\uff09\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\u78b1\u57fa\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\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    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        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*       ndata = 1     *\u8bbe\u7f6e\u8f93\u5165\u7684\u591a\u5e8f\u5217\u6bd4\u5bf9\u6587\u4ef6\u4e2d\u7684\u6570\u636e\u4e2a\u6570\u3002\n*       icode = 0     *\u8bbe\u7f6e\u9057\u4f20\u5bc6\u7801\u3002\u5f53\u8bbe\u7f6e\u53c2\u6570RateAncestor = 1\u65f6\u751f\u6548\uff0c\u6709\u5229\u4e8e\u6839\u636e\u5bc6\u7801\u5b50\u91cd\u6784\u7f16\u7801\u86cb\u767d\u7684\u7956\u5148DNA\u5e8f\u5217\u3002\n   Small_Diff = 7e-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\t  \n<b>*\u4f4d\u70b9\u66ff\u6362\u6a21\u578b\u53c2\u6570\uff1a<\/b>\n        nhomo = 1     *\u8bbe\u7f6e\u78b1\u57fa\u66ff\u6362\u6a21\u578b\u4e2d\u7684\u9891\u7387\u53c2\u6570\u8ba1\u7b97\u65b9\u6cd5\uff1a0\uff0c\u4f7f\u7528\u8f93\u5165\u6570\u636e\u4e2d\u7684\u89c2\u6d4b\u5230\u7684\u6240\u6709\u5e8f\u5217\u7684\u5e73\u5747\u78b1\u57fa\u9891\u7387\uff1b1\uff0c\u4f7f\u7528ML\u8fed\u4ee3\u65b9\u6cd5\u8ba1\u7b97\u78b1\u57fa\u9891\u7387Pi(T)\u3001Pi(C)\u3001Pi(A)\u548cPi(G)\uff0c\u9002\u5408model\u53c2\u6570\u503c\u4e3aF81\u3001F84\u3001HKY85\u3001T92\u3001T93\u6216REV\u6a21\u578b\uff1b2\uff0c\u8fdb\u5316\u6811\u6240\u6709\u7684\u5206\u679d\u5177\u6709\u76f8\u540c\u7684Kappa\u503c\uff0c\u9002\u5408K80\u3001F84\u548cHKY85\u8fd9\u4e09\u4e2a\u542b\u6709Kappa\u53c2\u6570\u7684\u6a21\u578b\uff1b3\uff0c\u5916\u90e8\u8282\u70b9\u6240\u5728\u7684\u5206\u679d\u4f7f\u7528\u4e00\u7ec4\u78b1\u57fa\u9891\u7387\uff0c\u6240\u6709\u5185\u90e8\u8282\u70b9\u6240\u5728\u5206\u679d\u4f7f\u7528\u4e00\u7ec4\u78b1\u57fa\u9891\u7387\uff0croot\u8282\u70b9\u6240\u5728\u5206\u679d\u4f7f\u7528\u4e00\u7ec4\u78b1\u57fa\u9891\u7387\uff0c\u4e5f\u79f0\u4e3aN1\u6a21\u578b\uff0c\u9700\u8981\u8f93\u5165\u6709\u6839\u6811\uff0c\u9002\u5408model\u53c2\u6570\u503c\u4e3aF84\u3001HKY85\u548cT95\u6a21\u578b\uff1b4\uff0croot\u8282\u70b9\u6240\u5728\u5206\u679d\u4f7f\u7528\u4e00\u7ec4\u78b1\u57fa\u9891\u7387\uff0c\u6240\u6709\u5176\u5b83\u5206\u679d\u4f7f\u7528\u4e00\u7ec4\u78b1\u57fa\u9891\u7387\uff0c\u4e5f\u79f0\u4e3aN2\u6a21\u578b\uff0c\u9700\u8981\u8f93\u5165\u6709\u6839\u6811\uff0c\u9002\u5408model\u53c2\u6570\u503c\u4e3aF84\u3001HKY85\u3001T95\u548cGTR\/REV\u6a21\u578b\uff1b5\uff0c\u8ba9\u7528\u6237\u81ea\u5df1\u5b9a\u4e49\u5404\u7ec4\u5206\u679d\u4f7f\u7528\u7684\u78b1\u57fa\u9891\u7387\uff0c\u9700\u8981\u5728\u8fdb\u5316\u6811\u4f7f\u7528#\u5bf9\u5404\u5206\u679d\u8fdb\u884c\u7f16\u53f7\u3002\n        model = 7     *\u9009\u53d6\u78b1\u57fa\u66ff\u6362\u6a21\u578b\u65b9\u6cd5\uff1a0\uff0cJC69\uff1b1\uff0cK80\uff1b2\uff0cF81\uff1b3\uff0cF84\uff1b4\uff0cHKY85\uff1b5\uff0cT92\uff1b6\uff0cTN93\uff1b7\uff0cREV\uff1b8\uff0cUNREST\uff1b9\uff0cREVu\uff1b10\uff0cUNRESTu\u3002\n                      *\u4e00\u822c\u4e3a\u4e86\u5f97\u5230\u8f83\u4e3a\u51c6\u786e\u7684\u679d\u957f\u4fe1\u606f\uff0c\u81f3\u5c11\u9009\u62e94\uff0c\u4f7f\u7528HKY85\u78b1\u57fa\u66ff\u6362\u6a21\u578b\uff0c\u7a0b\u5e8f\u4f1a\u4f7f\u7528ML\u65b9\u6cd5\u8ba1\u7b97Kappa\u503c\uff08\u8f6c\u6362\u7387\/\u98a0\u6362\u7387\u6bd4\u503c\uff09\u3002\n                      *\u63a8\u8350\u9009\u62e97\uff0c\u4e5f\u79f0\u4e3aGTR\uff0c\u7a0b\u5e8f\u4f1a\u4f7f\u7528ML\u8ba1\u7b97\u78b1\u57fa\u66ff\u6362\u6a21\u578b\u3002\n    fix_alpha = 0     *\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        alpha = 0.5   *\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\u78b1\u57fa\u66ff\u6362\u7387\u8f83\u9ad8\uff1b\u8be5\u503c\u8d8a\u5c0f\uff0c\u8868\u793a\u78b1\u57fa\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\u78b1\u57fa\u66ff\u6362\u7387\u65f6\u6052\u5b9a\u4e00\u81f4\u7684\u3002\n       Malpha = 0     *\u5f53\u8f93\u5165\u6570\u636e\u65f6\u591a\u57fa\u56e0\u65f6\uff0c\u8bbe\u7f6e\u8fd9\u4e9b\u57fa\u56e0\u4e4b\u95f4\u7684alpha\u662f\u5426\u4e0d\u4e00\u81f4\uff1a1\uff0c\u4e0d\u540c\u57fa\u56e0\u4e4b\u95f4\u5177\u6709\u4e0d\u540c\u7684alpha\u503c\uff1b0\uff0c\u6240\u6709\u57fa\u56e0\u90fd\u5177\u6709\u76f8\u540c\u7684alpha\u503c\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        nparK = 0     *\u8bbe\u7f6erate-class models\uff1a1\uff0c\u4e0d\u540c\u4f4d\u70b9\u7684\u53d8\u5f02\u901f\u7387\u662f\u72ec\u7acb\u7684\uff0c\u9650\u5b9ancatG\u5404\u7c7b\u7684\u6982\u7387\u90fd\u76f8\u7b49\uff1b2\uff0c\u4e0d\u540c\u4f4d\u70b9\u7684\u53d8\u5f02\u901f\u7387\u662f\u72ec\u7acb\u7684\uff0c\u4e0d\u9650\u5b9ancatG\u5404\u7c7b\u7684\u6982\u7387\u90fd\u76f8\u7b49\uff1b3\uff0c\u90bb\u8fd1\u4f4d\u70b9\u7684\u53d8\u5f02\u901f\u7387\u662fMarkov\u76f8\u5173\u7684\uff0c\u9650\u5b9ancatG\u5404\u7c7b\u7684\u6982\u7387\u90fd\u76f8\u7b49\uff1b4\uff0c\u90bb\u8fd1\u4f4d\u70b9\u7684\u53d8\u5f02\u901f\u7387\u662fMarkov\u76f8\u5173\u7684\uff0c\u4e0d\u9650\u5b9ancatG\u5404\u7c7b\u7684\u6982\u7387\u90fd\u76f8\u7b49\u3002\u6b64\u5916\uff0c\u8bbe\u7f6e\u8be5\u53c2\u6570\u503c\u4e0d\u4e3a0\uff0c\u6bd4\u8f83\u6d88\u8017\u8ba1\u7b97\u5e76\u4e14\u8981\u6c42nhomo = 0\uff0c\u5426\u5219\u7a0b\u5e8f\u62a5\u9519\u3002\n    fix_kappa = 0     *\u8bbe\u7f6e\u662f\u5426\u7ed9\u5b9a\u4e00\u4e2aKappa\u503c\uff08\u8be5\u53c2\u6570\u5728model\u8bbe\u7f6e\u4e3aK80\u3001F84\u6216HKY85\u65f6\u6709\u6548\uff09\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\u5bf9\u4e8eJC69\u548cF81\uff0c\u8be5\u53c2\u6570\u6ca1\u6709\u6548\u679c\uff1b\u5bf9\u4e8eTN93\u548cREV\uff0c\u5219\u5206\u522b\u5bf9\u5e942\u4e2a\u548c5\u4e2arate\u53c2\u6570\u3002\n        kappa = 5     *\u8bbe\u7f6e\u4e00\u4e2a\u56fa\u5b9a\u7684Kappa\u503c\uff0c\u6216\u4e00\u4e2a\u521d\u59cb\u7684Kappa\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\u884cbaseml\u547d\u4ee4\u5bf9\u6838\u9178\u5e8f\u5217\u8fdb\u884c\u8fdb\u5316\u53c2\u6570\u8ba1\u7b97<\/h2>\n\n\n\n<p>\u7a0b\u5e8f\u8fd0\u884c\u7684\u547d\u4ee4\uff1a<\/p>\n\n\n\n<pre class=\"wp-block-code\"><code>baseml baseml.ctl<\/code><\/pre>\n\n\n\n<h2>5. \u7ed3\u679c\u6587\u4ef6\u89e3\u91ca<\/h2>\n\n\n\n<p>\u7a0b\u5e8f\u7684\u4e3b\u8981\u7ed3\u679c\u6587\u4ef6\u662fmlb\uff0c\u5176\u4e3b\u8981\u5185\u5bb9\u6709\uff1a<\/p>\n\n\n\n<pre class=\"wp-block-preformatted\">1. \u56db\u79cd\u78b1\u57fa\u89c2\u6d4b\u5230\u7684\u9891\u7387\u53ca\u5176\u5e73\u5747\u503c\u3002<br>2. \u5404\u5e8f\u5217\u4e4b\u95f4\u7684\u8ddd\u79bb\u77e9\u9635\u3002<br>3. \u5404\u5206\u679d\u7684\u957f\u5ea6\u3001\u603b\u7684\u679d\u957f\u3001\u542b\u6709\u679d\u957f\u4fe1\u606f\u7684\u7cfb\u7edf\u53d1\u80b2\u6811\u3002<br>4. ML\u8ba1\u7b97\u51fa\u6765\u7684\u78b1\u57fa\u9891\u7387\u3002<br>5. \u78b1\u57fa\u66ff\u6362\u77e9\u9635\u3002<br>6. 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