{"id":2948,"date":"2019-09-19T20:04:39","date_gmt":"2019-09-19T12:04:39","guid":{"rendered":"http:\/\/www.chenlianfu.com\/?p=2948"},"modified":"2019-10-23T16:33:23","modified_gmt":"2019-10-23T08:33:23","slug":"%e4%bd%bf%e7%94%a8paml%e8%bf%9b%e8%a1%8c%e6%ad%a3%e9%80%89%e6%8b%a9%e5%9f%ba%e5%9b%a0%e5%88%86%e6%9e%90","status":"publish","type":"post","link":"http:\/\/www.chenlianfu.com\/?p=2948","title":{"rendered":"\u7cfb\u7edf\u53d1\u80b2\u5206\u6790\u8f6f\u4ef6PAML\u7684\u5b89\u88c5\u548c\u7b80\u4ecb"},"content":{"rendered":"\n

PAML (Phylogenetic Analysis by Maximum Likelihood)\uff0c\u662f\u6768\u5b50\u6052\u5f00\u53d1\u7684\u4e00\u6b3e\u5229\u7528DNA\u6216Protein\u6570\u636e\u4f7f\u7528\u6700\u5927\u4f3c\u7136\u6cd5\u8fdb\u884c\u7cfb\u7edf\u53d1\u80b2\u5206\u6790\u7684\u8f6f\u4ef6\u3002<\/p>\n\n\n\n

\u8be5\u8f6f\u4ef6\u4e0d\u64c5\u957f\u6784\u6811\uff0c\u4f46\u80fd\u7528\u4e8e\u8bc4\u4f30\u7cfb\u7edf\u8fdb\u5316\u8fc7\u7a0b\u4e2d\u7684\u53c2\u6570\u548c\u5047\u8bbe\u68c0\u9a8c\uff0c\u6709\u5229\u4e8ePAUP\u3001PHYLIP\u3001MOLPHY\u3001PHyML\u548cRAxML\u7b49\u5176\u5b83\u8f6f\u4ef6\u7684\u6784\u6811\u3002 PAML\u8f6f\u4ef6\u7684baseml\u548ccodeml\u547d\u4ee4\u4e2d\u7528\u4e8e\u641c\u7d22\u7cfb\u7edf\u53d1\u80b2\u6811\u7684\u7b97\u6cd5\u975e\u5e38\u539f\u59cb\u4e14\u6548\u679c\u8f83\u5dee\uff0c\u5f53\u6570\u636e\u91cf\u8f83\u5927\uff0c\u4f8b\u5982\u7269\u79cd\u6570\u591a\u4e8e10\u4e2a\u65f6\uff0c\u4f5c\u8005\u63a8\u8350\u4f7f\u7528\u5176\u4ed6\u66f4\u597d\u7684\u8f6f\u4ef6\u6765\u6784\u5efa\u7cfb\u7edf\u53d1\u80b2\u6811\u3002 \u8f6f\u4ef6\u7684\u8be6\u7ec6\u7528\u6cd5\u8bf7\u53c2\u8003PDF\u8bf4\u660e\u6587\u6863<\/a>\u53ca\u5e38\u89c1\u95ee\u9898<\/a>\u3002 <\/p>\n\n\n\n

\u4e0b\u8f7d\u5e76\u5b89\u88c5PAML\u8f6f\u4ef6<\/p>\n\n\n\n

$ wget http:\/\/abacus.gene.ucl.ac.uk\/software\/paml4.9i.tgz
$ tar zxf paml4.9i.tgz -C \/opt\/biosoft\/
$ cd \/opt\/biosoft\/paml4.9i\/
$ rm bin\/*
$ cd src
$ make -f Makefile
$ cp baseml basemlg chi2 codeml evolver infinitesites mcmctree pamp yn00 ..\/bin
$ echo 'PATH=$PATH:\/opt\/biosoft\/paml4.9i\/bin' >> ~\/.bashrc
$ source ~\/.bashrc
<\/pre>\n\n\n\n
PAML\u8f6f\u4ef6\u5305\u542b\u591a\u652f\u7a0b\u5e8f\uff0c\u6765\u5b9e\u73b0\u4e0d\u540c\u7684\u7cfb\u7edf\u53d1\u80b2\u5206\u6790\u529f\u80fd\uff1a<\/p>\n\n\n\n
baseml \u7528\u4e8e\u5bf9\u6838\u9178\u5e8f\u5217\u8fdb\u884c\u6700\u5927\u4f3c\u7136\u6cd5\u5206\u6790\u3002
codeml \u7528\u4e8e\u5bf9\u5bc6\u7801\u5b50\u548c\u86cb\u767d\u5e8f\u5217\u8fdb\u884c\u6700\u5927\u4f3c\u7136\u6cd5\u5206\u6790\u3002\u8be5\u7a0b\u5e8f\u6574\u5408\u4e86\u4ee5\u524d\u7684\u4e24\u652f\u7a0b\u5e8fcodonml\u548caaml\uff0c\u524d\u8005\u7528\u4e8e\u5bf9\u5bc6\u7801\u5b50\u5e8f\u5217\u8fdb\u884c\u5206\u6790\uff0c\u540e\u8005\u5bf9\u86cb\u767d\u5e8f\u5217\u8fdb\u884c\u5206\u6790\u3002\u5728\u65b0\u7684codeml\u7a0b\u5e8f\u7684\u914d\u7f6e\u6587\u4ef6\u4e2d\u8bbe\u7f6eseqtype=1\uff0c\u8868\u793a\u4f7f\u7528codonml\u547d\u4ee4\uff0c\u8bbe\u7f6eseqtype=2\uff0c\u8868\u793a\u4f7f\u7528aaml\u547d\u4ee4\u3002
evolver \u7528\u4e8e\u6a21\u62df\u6838\u9178\u3001\u5bc6\u7801\u5b50\u6216\u86cb\u767d\u5e8f\u5217\u3002
basemlg \u76f8\u6bd4\u4e8ebaseml\uff0c\u8be5\u7a0b\u5e8f\u5e94\u7528\u4e86\u8fde\u7eed\u7684gamma\u6a21\u578b\u3002\u5f53\u6570\u636e\u4e2d\u7684\u7269\u79cd\u6570\u591a\u4e8e6\u52307\u4e2a\u65f6\uff0c\u8be5\u7a0b\u5e8f\u8fd0\u884c\u975e\u5e38\u6162\u4ee5\u81f3\u5f97\u4e0d\u5230\u7ed3\u679c\u3002\u8fd9\u65f6\uff0c\u9700\u8981\u4f7f\u7528\u8bbe\u7f6e\u79bb\u6563gamma\u6a21\u578b\u7684baseml\u547d\u4ee4\u3002
mcmctree \u8be5\u7a0b\u5e8f\u5e94\u7528Bayesian MCMC\u7b97\u6cd5\u8ba1\u7b97\u7269\u79cd\u5206\u6b67\u65f6\u95f4\u3002
pamp  \u7528\u4e8e\u7b80\u7ea6\u6cd5\u5206\u6790\u3002
yn00  \u7528\u4e8e\u5bf9\u4e24\u6761\u7f16\u7801\u86cb\u767d\u7684DNA\u5e8f\u5217\u8fdb\u884c\u6bd4\u8f83\u5e76\u8ba1\u7b97dnds\u3002
chi2  \u7528\u4e8e\u5728likelihood ratio test\u4e2d\u8ba1\u7b97\u5361\u65b9\u4e34\u754c\u503c\u548cp\u503c\u3002<\/pre>\n\n\n\n
PAML\u4f7f\u7528\u524d\u7684\u6ce8\u610f\u4e8b\u9879\uff1a<\/p>\n\n\n\n
1. PAML\u8981\u6c42\u7684\u8f93\u5165\u6587\u4ef6\u662f\u591a\u5e8f\u5217\u6bd4\u5bf9\u7ed3\u679c\u3002PAML\u8f6f\u4ef6\u4e0d\u80fd\u8fdb\u884c\u591a\u5e8f\u5217\u6bd4\u5bf9\uff0c\u9700\u8981\u4f7f\u7528\u5176\u4ed6\u8f6f\u4ef6\u8fdb\u884c\u5206\u6790\u3002
2. PAML\u8f6f\u4ef6\u8fdb\u884c\u57fa\u4e8e\u5bc6\u7801\u5b50\u7684\u5206\u6790\u8981\u6c42\u8f93\u5165\u7684\u5e8f\u5217\u5fc5\u987b\u662f\u53bb\u9664\u4e86Introns\u7b49\u975e\u7f16\u7801\u533a\u7684DNA\u5e8f\u5217\uff0c\u4e14\u5176\u957f\u5ea6\u662f3\u7684\u6574\u6570\u500d\uff0c\u4e14\u7b2c\u4e00\u4e2a\u6838\u9178\u4f4d\u70b9\u662f\u5bc6\u7801\u5b50\u7684\u7b2c\u4e00\u4f4d\u3002PAML\u8f6f\u4ef6\u4e0d\u80fd\u8fdb\u884c\u57fa\u56e0\u9884\u6d4b\uff0c\u5bc6\u7801\u5b50\u7684\u6bd4\u5bf9\u7ed3\u679c\u9700\u8981\u81ea\u884c\u7f16\u5199\u7a0b\u5e8f\u5206\u6790\u5f97\u5230\u3002
3. \u5bf9\u4e8e\u8f83\u5927\u6570\u636e\uff08\u7269\u79cd\u6570>=10\uff09\u91cf\u7684\u5206\u6790\uff0c\u8f93\u5165\u7684\u6811\u6587\u4ef6\u6700\u597d\u4f7f\u7528\u5176\u4ed6\u8f6f\u4ef6\u8ba1\u7b97\u3002<\/pre>\n\n\n\n
1. \u4f7f\u7528codeml\u548c\u8fdb\u884c\u6b63\u9009\u62e9\u5206\u6790<\/h2>\n\n\n\n
CodonFreq<\/p>\n\n\n\n
\u7a0b\u5e8f\u6839\u636e\u8f93\u5165\u7684\u5e8f\u5217\u8ba1\u7b97\u51fa\u5bc6\u7801\u5b503\u4e2a\u4f4d\u70b9\u4e0a\u54044\u79cd\u78b1\u57fa\u7684\u9891\u7387\uff0c\u4f8b\u5982\uff1a

Codon position x base (3x4) table, overall
 position  1:    T:0.20110    C:0.13736    A:0.32308    G:0.33846
 position  2:    T:0.20000    C:0.17143    A:0.33077    G:0.29780
 position  3:    T:0.32747    C:0.22857    A:0.25165    G:0.19231
 Average         T:0.24286    C:0.17912    A:0.30183    G:0.27619

\u7136\u540e\u518d\u8ba1\u7b9764\u79cd\u5bc6\u7801\u5b50\u7684\u9891\u7387\u3002\u8ba1\u7b97\u65b9\u6cd5\u6709\u56db\u79cd\uff1a
\uff081\uff09\u8bbe\u7f6eCodonFreq\u53c2\u6570\u503c\u4e3a0\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\uff1b
\uff082\uff09\u8bbe\u7f6eCodonFreq\u53c2\u6570\u503c\u4e3a1\uff08F1X4\uff09\uff0c\u8868\u793a\u9664\u4e09\u79cd\u7ec8\u6b62\u5bc6\u7801\u5b50\u9891\u7387\u4e3a0\uff0c\u8ba1\u7b9761\u79cd\u5bc6\u7801\u5b50\u65f6\uff0c\u4f7f\u7528\u4e0a\u9762Average\u7684\u503c\u8fdb\u884c\u8ba1\u7b97\uff0c\u4f8b\u5982TTC\u5bc6\u7801\u5b50\u7684\u9891\u7387\u4e3a0.24286*0.24286*0.17912\uff1b\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\u3002
\uff083\uff09\u8bbe\u7f6eCodonFreq\u53c2\u6570\u503c\u4e3a2\uff08F3X4\uff09\uff0c\u8868\u793a\u9664\u4e09\u79cd\u7ec8\u6b62\u5bc6\u7801\u5b50\u9891\u7387\u4e3a0\uff0c\u8ba1\u7b9761\u79cd\u5bc6\u7801\u5b50\u65f6\uff0c\u4f7f\u7528\u4e0a\u9762\u4e09\u79cdposition\u7684\u7684\u503c\u8fdb\u884c\u8ba1\u7b97\uff0c\u4f8b\u5982TTC\u5bc6\u7801\u5b50\u7684\u9891\u7387\u4e3a 0.20110*0.20110*0.22857\uff1b\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\u3002 
\uff084\uff09\u8bbe\u7f6eCodonFreq\u53c2\u6570\u503c\u4e3a3\uff08codon table\uff09\uff0c\u8868\u793a\u76f4\u63a5\u4f7f\u7528\u89c2\u6d4b\u5230\u7684\u5404\u5bc6\u7801\u5b50\u7684\u603b\u7684\u9891\u6570\/\u6240\u6709\u5bc6\u7801\u503c\u5f97\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<\/pre>\n","protected":false},"excerpt":{"rendered":"
PAML (Phylogenetic Analysis by Maximum L … \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\/2948"}],"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=2948"}],"version-history":[{"count":7,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2948\/revisions"}],"predecessor-version":[{"id":3002,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2948\/revisions\/3002"}],"wp:attachment":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=2948"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=2948"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=2948"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}