{"id":61227,"date":"2024-10-28T14:07:38","date_gmt":"2024-10-28T06:07:38","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=61227"},"modified":"2024-10-28T14:07:38","modified_gmt":"2024-10-28T06:07:38","slug":"%e9%94%99%e8%bf%87%e7%9c%9f%e7%9a%84%e4%bc%9a%e5%90%8e%e6%82%94%ef%bc%81%e4%b8%89%e5%88%86%e9%92%9f%e6%95%99%e4%bd%a0%e7%94%a8iqtree%e6%9e%84%e5%bb%ba%e4%b8%80%e4%b8%aa%e5%ae%8c%e7%be%8e%e7%9a%84","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=61227","title":{"rendered":"\u9519\u8fc7\u771f\u7684\u4f1a\u540e\u6094\uff01\u4e09\u5206\u949f\u6559\u4f60\u7528IQTree\u6784\u5efa\u4e00\u4e2a\u5b8c\u7f8e\u7684\u8fdb\u5316\u6811\uff01\u4ee3\u7801\u7b80\u5355+\u81ea\u52a8\u9009\u62e9\u6700\u4f73\u6a21\u578b\uff0c\u7cfb\u7edf\u53d1\u80b2\u5206\u6790\u5982\u6b64\u7b80\u5355\uff01"},"content":{"rendered":"\n

<\/p>\n\n\n\n

\"\"<\/figure>\n\n\n\n

\u55e8\uff0c\u6211\u662f\u5c0f\u5e08\u59b9\uff0c\u5f88\u9ad8\u5174\u80fd\u591f\u548c\u5927\u5bb6\u4e00\u8d77\u6765\u5b66\u4e60\u751f\u7269\u4fe1\u606f\u5b66\u3002\u524d\u51e0\u5929\u5c0f\u5e08\u59b9\u7ed9\u5927\u5bb6\u5e26\u6765\u4e86\u591a\u5e8f\u5217\u6bd4\u5bf9\u5de5\u5177mafft\u7684\u5206\u4eab\u3002\u4eca\u5929\uff0c\u5c0f\u5e08\u59b9\u5c31\u7ee7\u7eed\u5e26\u6765\u7cfb\u7edf\u53d1\u80b2\u5206\u6790\u4e00\u7ad9\u5f0f\u7684\u5206\u4eab\uff01\u4eca\u5929\u7ed9\u5927\u5bb6\u4ecb\u7ecd\u7684\u662f\u4e00\u4e2a\u975e\u5e38\u5f3a\u5927\u7684\u5de5\u5177\u2014\u2014IQ-TREE2\u3002\u672c\u6b21\u4ecb\u7ecd\u7684\u8f6f\u4ef6\u64cd\u4f5c\u5360\u7528\u5185\u5b58\u6bd4\u8f83\u5927\uff0c\u5efa\u8bae\u4f7f\u7528\u670d\u52a1\u5668\uff0c\u6b22\u8fce\u8054\u7cfb\u5c0f\u5e08\u59b9\u79df\u8d41\u6027\u4ef7\u6bd4\u5c45\u9ad8\u7684\u670d\u52a1\u5668~<\/strong><\/p>\n\n\n\n

\"\"<\/figure>\n\n\n\n

\u505a\u9057\u4f20\u8fdb\u5316\u7684\u670b\u53cb\u80af\u5b9a\u5bf9\u8fdb\u5316\u6811\u4e0d\u4f1a\u964c\u751f\uff0c\u73b0\u5728\u6587\u732e\u5e02\u573a\u4e0a\u505a\u7cfb\u7edf\u53d1\u80b2\u7684\u8fd9\u4e48\u591a\uff0c\u8981\u95ee\u8fdb\u5316\u6811\u6784\u5efa\u54ea\u5bb6\u5f3a\uff0c\u516c\u4f17\u53f7\u5173\u6ce8R\u8bed\u8a00\u5b66\u5f92\u627e\u7b54\u6848\u3002IQ-TREE2\u4e13\u4e3a\u7cfb\u7edf\u53d1\u80b2\u63a8\u65ad\u800c\u8bbe\u8ba1\uff0c\u63d0\u4f9b\u4e86\u5feb\u901f\u51c6\u786e\u7684\u6811\u91cd\u5efa\u529f\u80fd\u3002\u8fd9\u6b3e\u8f6f\u4ef6\u4ee5\u5176\u9ad8\u6548\u7684\u7b97\u6cd5\u548c\u7528\u6237\u53cb\u597d\u7684\u754c\u9762\uff0c\u4f7f\u5f97\u5373\u4f7f\u662f\u5904\u7406\u5927\u89c4\u6a21\u6570\u636e\u96c6\u4e5f\u53d8\u5f97\u8f7b\u677e\u5feb\u6377\u3002\u8fdb\u5316\u6811\u53ef\u96be\u4e0d\u5012\u751f\u4fe1\u9ad8\u624b\u5c0f\u5e08\u59b9\uff0c\u8981\u662f\u540c\u5b66\u4eec\u6709\u81ea\u5df1\u505a\u4e0d\u4e86\u7684\u751f\u4fe1\u5206\u6790\uff0c\u6b22\u8fce\u968f\u65f6\u8054\u7cfb\u6211\uff01\uff01\uff01<\/strong>\u3002<\/p>\n\n\n\n

\u81ea2013\u5e74\u63a8\u51fa\u4ee5\u6765\uff0ciqtree\u4ee5\u5176\u5feb\u901f\u7cbe\u51c6\u7684\u5efa\u6811\u548c\u5168\u9762\u7684\u529f\u80fd\u5728\u7ade\u4e89\u6fc0\u70c8\u7684\u7cfb\u7edf\u53d1\u80b2\u6811\uff08phylogenetics\uff09\u9886\u57df\u5feb\u901f\u8e7f\u7ea2\uff0c\u5e76\u5e7f\u53d7\u597d\u8bc4\uff0c\u76ee\u524d\u780d\u4e0b\u8c37\u6b4c\u5b66\u672f8748\u6b21\u5f15\u7528\u3002<\/p>\n\n\n\n

\"\"<\/figure>\n\n\n\n

\u56fe1 \u5de5\u5177\u5f15\u7528\u60c5\u51b5<\/p>\n\n\n\n

IQ-TREE2\u7684\u6838\u5fc3\u7279\u70b9\u5305\u62ec\uff1a<\/p>\n\n\n\n

1.\u9ad8\u6548\u7684\u6811\u91cd\u5efa<\/strong>\uff1a\u91c7\u7528\u5feb\u901f\u6709\u6548\u7684\u968f\u673a\u7b97\u6cd5\uff0c\u901a\u8fc7\u6700\u5927\u4f3c\u7136\u63a8\u65ad\u7cfb\u7edf\u53d1\u80b2\u6811\uff0c\u8ba1\u7b97\u65f6\u95f4\u4e0a\u4f18\u4e8eRAxML\u548cPhyML\u3002<\/p>\n\n\n\n

2.ModelFinder<\/strong>\uff1a\u8fd9\u662f\u4e00\u4e2a\u5feb\u901f\u51c6\u786e\u7684\u6a21\u578b\u9009\u62e9\u5de5\u5177\uff0c\u652f\u6301\u81ea\u7531\u901f\u7387\u53d8\u5316\u6a21\u578b\uff0c\u5e76\u4e14\u6bd4jModelTest\u548cProtTest\u5feb10\u5230100\u500d\u3002\u5b83\u8fd8\u80fd\u627e\u5230\u6700\u5408\u9002\u7684\u5206\u533a\u65b9\u6848\u3002<\/p>\n\n\n\n

3.UFBoot<\/strong>\uff1a\u63d0\u4f9b\u8fd1\u4f3c\u65e0\u504f\u7684\u5206\u652f\u652f\u6301\u503c\uff0c\u8fd0\u884c\u901f\u5ea6\u6bd4\u975e\u53c2\u6570\u5f15\u5bfc\u7a0b\u5e8f\u5feb100\u500d\uff0c\u6bd4RAxML\u5feb\u901f\u5f15\u5bfc\u7a0b\u5e8f\u5feb10\u523040\u500d\u3002<\/p>\n\n\n\n

4.AliSim<\/strong>\uff1aAliSim\uff08\u6bd4\u5bf9\u6a21\u62df\u5668\uff09\u5141\u8bb8\u5728\u6bd4 Seq-Gen \u548c INDELible \u66f4\u771f\u5b9e\u7684\u6a21\u578b\u4e0b\u5feb\u901f\u6a21\u62df\u591a\u5e8f\u5217\u6bd4\u5bf9\u3002<\/p>\n\n\n\n

\"\"<\/figure>\n\n\n\n

\u56fe2 IQTREE\u5de5\u5177\u7684\u4eae\u70b9<\/p>\n\n\n\n

\u4e00\u3001\u4e0b\u8f7d\u548c\u5b89\u88c5<\/strong><\/strong><\/p>\n\n\n\n

$ wget -c https:\/\/github.com\/iqtree\/iqtree2\/releases\/download\/v2.1.3\/iqtree-2.1.3-Linux.tar.gz<\/strong><\/strong><\/p>\n\n\n\n

$ tar -zxvf iqtree-2.1.3-Linux.tar.gz<\/strong><\/strong><\/p>\n\n\n\n

$ echo ‘export PATH=”~\/iqtree-2.1.3-Linux\/bin:$PATH”‘>>~\/.bashrc<\/strong><\/strong><\/p>\n\n\n\n

$ source .bashrc<\/strong><\/strong><\/p>\n\n\n\n

\u89e3\u538b\u540eiqtree\u6267\u884c\u6587\u4ef6\u5c31\u5728bin\/\u76ee\u5f55\u4e0b\uff0c\u8fdb\u5165iqtree-2.1.3-Linux\u76ee\u5f55\u540e\u8fd8\u6709\u4e00\u4e2a\u793a\u4f8b\u6587\u4ef6example.phy\u3002<\/p>\n\n\n\n

\u4e8c\u3001\u5e38\u7528\u547d\u4ee4<\/strong><\/strong><\/p>\n\n\n\n

1.\u9009\u62e9\u6700\u4f73\u6a21\u578b<\/strong><\/p>\n\n\n\n

IQTREE2\u5185\u7f6e\u4e86\u4e0a\u767e\u79cd\u6a21\u578b\uff0c\u4f5c\u4e3a\u5c0f\u767d\u7684\u6211\u4eec\u5e94\u8be5\u5982\u4f55\u9009\u62e9\u5462\uff0c\u4e0d\u7528\u62c5\u5fc3\uff0c\u6211\u4eec\u53ef\u4ee5\u5229\u7528ModelFinder\u529f\u80fd\u8fdb\u884c\u6700\u4f73\u6a21\u578b\u9009\u62e9\uff0c\u53c2\u6570-m\u8bbe\u7f6eMF\u81ea\u52a8\u9009\u62e9\u6700\u4f73\u6a21\u578b\u4f46\u4e0d\u5efa\u6811\uff1b\u53c2\u6570-m\u8bbe\u7f6eMFP\u81ea\u52a8\u68c0\u6d4b\u6700\u4f73\u6a21\u578b\u5e76\u5efa\u6811\u3002<\/p>\n\n\n\n

$ iqtree2 -s example.phy -m MF<\/strong><\/strong><\/p>\n\n\n\n

\"\"<\/figure>\n\n\n\n

\u56fe3 ModelFinder\u7ed3\u679c\u6587\u4ef6<\/p>\n\n\n\n

Iqtree\u4f1a\u6d4b\u8bd5\u591a\u8fbe546\u4e2a\u86cb\u767d\u6a21\u578b\u5e76\u7ed9\u51fa\u6700\u4f73\u6a21\u578b\uff0c\u6253\u5f00\u540e\u7f00\u540d\u4e3amodel.gz\uff0c\u7ed3\u679c\u5982\u56fe4\u6240\u793a\uff1a<\/p>\n\n\n\n

$ zcat example.phy.model.gz | less<\/strong><\/strong><\/p>\n\n\n\n

\"\"<\/figure>\n\n\n\n

\u56fe4 ModelFinder\u7ed3\u679c\u793a\u610f\u56fe<\/p>\n\n\n\n

\u6211\u4eec\u627e\u5230\u7ea2\u8272\u65b9\u6846\u6807\u6ce8\u90e8\u5206\uff0c\u5c31\u662fModelFinder\u7684\u6700\u7ec8\u7ed3\u679c\u3002\u4f9d\u636eAIC\u51c6\u5219\uff0c\u6700\u4f73\u7684\u66ff\u6362\u6a21\u578b\u5e94\u8be5\u4e3aGTR+F+I+G4\uff1b\u4f9d\u636eBIC\u51c6\u5219\uff0c\u6700\u4f73\u7684\u66ff\u6362\u6a21\u578b\u4e3aTIM2+F+I+G4\u3002\u6211\u4eec\u53ef\u4ee5\u4f9d\u636e\u4e2a\u4eba\u7684\u7814\u7a76\u9700\u6c42\u4ee5\u53ca\u4e0b\u4e00\u6b65\u7684\u5de5\u4f5c\u9009\u62e9\u5408\u9002\u7684\u51c6\u5219\uff0c\u5982\u679c\u9700\u8981\u8fdb\u884c\u8d1d\u53f6\u65af\u63a8\u65ad\uff08\u6784\u5efaMCMC\u7cfb\u7edf\u53d1\u80b2\u6811\uff09\uff0c\u90a3\u6211\u4eec\u5e94\u8be5\u91c7\u7528\u8d1d\u53f6\u65af\uff08BIC\uff09\u51c6\u5219\u3002<\/p>\n\n\n\n

\u6b64\u5916\u8fd8\u6709\uff1a<\/p>\n\n\n\n

example.phy.iqtree\uff1a\u4e3b\u8981\u62a5\u544a\u6587\u4ef6\uff0c\u6211\u4eec\u53ef\u4ee5\u67e5\u770b\u6b64\u6587\u4ef6\u4ee5\u67e5\u770b\u8ba1\u7b97\u7ed3\u679c\u3002\u5b83\u8fd8\u5305\u542b\u6700\u7ec8\u6811\u7684\u6587\u672c\u8868\u793a\uff08\u89c1\u4e0b\u6587\uff09\u3002<\/p>\n\n\n\n

example.phy.treefile\uff1aNEWICK\u683c\u5f0f\u7684ML\u6811\uff0c\u53ef\u4ee5\u901a\u8fc7\u4efb\u4f55\u652f\u6301\u7684\u6811\u67e5\u770b\u5668\u7a0b\u5e8f\uff08\u5982FigTree\u6216iTOL\uff09\u8fdb\u884c\u53ef\u89c6\u5316\u3002<\/p>\n\n\n\n

example.phy.log\uff1a\u6574\u4e2a\u8fd0\u884c\u7684\u65e5\u5fd7\u6587\u4ef6\u3002<\/p>\n\n\n\n

$ less example.phy.iqtree<\/p>\n\n\n\n

\"\"<\/figure>\n\n\n\n

\u56fe5 example.phy.iqtree\u4e3b\u8981\u62a5\u544a\u6587\u4ef6<\/p>\n\n\n\n

2.\u6784\u5efa\u7cfb\u7edf\u53d1\u80b2\u6811<\/strong><\/strong><\/p>\n\n\n\n

\u5f97\u5230\u4e86\u6700\u4f73\u6a21\u578b\u4e4b\u540e\uff0c\u5c31\u53ef\u4ee5\u8fdb\u884c\u7cfb\u7edf\u53d1\u80b2\u6811\u7684\u6784\u5efa\u4e86\uff0c\u8fd9\u91cc\u9009\u62e9\u7684\u662f\u8d64\u6c60\u4fe1\u606f\uff08AIC\uff09\u51c6\u5219\u9009\u62e9\u7684\u6700\u4f73\u6a21\u578b\u3002<\/p>\n\n\n\n

$ iqtree2 -s example.phy -m GTR+F+I+G4  <\/strong><\/strong><\/p>\n\n\n\n

3.\u5176\u4ed6\u547d\u4ee4<\/strong><\/strong><\/p>\n\n\n\n

\u76f4\u63a5\u9009\u62e9\u6700\u4f73\u7684\u6a21\u578b\u8fdb\u884c\u6811\u7684\u6784\u5efa\uff0c\u4e0d\u8fdb\u884cbootstrap\uff1a<\/p>\n\n\n\n

$ iqtree.exe -s example.phy -m MFP  <\/strong><\/strong><\/p>\n\n\n\n

\u8fdb\u884c\u6700\u4f73\u6a21\u578b\u6784\u5efa\u6811\uff0c\u5e76\u4e14\u8fdb\u884cbootstrap\uff1a<\/p>\n\n\n\n

$ iqtree.exe -s example.phy -m MFP -b 1000 -nt AUTO<\/strong><\/strong><\/p>\n\n\n\n

\u8fdb\u884cGTR+F+I+G4\u6a21\u578b\u6784\u5efa\u7cfb\u7edf\u53d1\u80b2\u6811\uff1a<\/p>\n\n\n\n

$ iqtree.exe -s example.phy -m GTR+F+I+G4 -b 1000 -nt AUTO <\/strong><\/strong><\/p>\n\n\n\n

\u91cd\u62bd\u6837\u52a0\u901f\uff0c\u7ed3\u679c\u65e0\u5dee\u5f02\uff0c\u4f46\u662f\u8017\u65f6\u76f8\u5bf9\u5c11\u4e00\u4e9b\uff1a<\/p>\n\n\n\n

$ iqtree.exe -s example.phy -m GTR+F+R3 -b 1000 -bnni -nt AUTO -redo<\/strong><\/strong><\/p>\n\n\n\n

\u4f7f\u75284\u4e2a CPU \u6838\u6765\u52a0\u901f\u8ba1\u7b97:<\/p>\n\n\n\n

$ iqtree -s example.phy  -T 4<\/strong><\/strong><\/p>\n\n\n\n

\u57fa\u4e8eIQTree\u7684UFBoot2\u8fdb\u884c\u6253\u5206\uff0c\u8fd9\u4e2a\u6253\u5206\u5e76\u4e0d\u662f\u666e\u901a\u7684Bootstrap\u81ea\u5c55\u503c\uff0c\u800c\u662f\u4e00\u79cd\u8fd1\u4f3c\u503c\uff0c\u901f\u5ea6\u4f1a\u5feb\u5f88\u591a\uff0c\u4f46\u8981\u572895%\u4ee5\u4e0a\u7684UFBoot\u624d\u53ef\u4fe1\u3002\u5982\u679c\u60f3\u8981\u6539\u6210\u666e\u901a\u7684Bootstrap\u503c\uff0c\u5219\u6539\u6210-b 100\uff0c\u6211\u4eec\u5e73\u65f6\u67e5\u770b\u8fdb\u5316\u6811\u53ef\u4ee5\u4e0d\u8bbe\u7f6e\u81ea\u5c55\u503c\uff0c\u4f46\u662f\u5982\u679c\u8981\u53d1\u8868\u6587\u732e\uff0c\u8981\u8bb0\u5f97\u8bbe\u7f6e1000\u4ee5\u4e0a\u7684\u81ea\u5c55\u503c\uff0c\u7f16\u8f91\u624d\u4f1a\u8ba4\u540c\u54e6<\/strong>~<\/h1>\n\n\n\n

$ iqtree -s example.phy -m MFP -B 1000<\/strong><\/strong><\/p>\n\n\n\n

–symtest\uff1a\u76ee\u524d\u4e00\u822c\u7684\u5efa\u6811\u65b9\u6cd5\uff0c\u90fd\u662f\u57fa\u4e8e\u6240\u8c13\u7684SRH\u539f\u5219\uff0c\u5373stationary, reversible, and homogeneous\uff0c\u5bf9\u4e8eSRH\u539f\u5219\u7684\u8fdd\u80cc\u5728\u6587\u732e\u4e2d\u5341\u5206\u666e\u904d\uff0c\u5efa\u51fa\u6765\u7684\u6811\u662f\u5426\u771f\u7684\u53ef\u9760\u5c31\u8981\u6253\u4e0a\u95ee\u53f7\u4e86\u3002\u4f60\u7684dataset\u662f\u5426\u5b58\u5728\u5bf9\u8be5\u539f\u5219\u7684\u8fdd\u80cc\u5462\uff1f\u4e0d\u59a8\u7528–symtest\u68c0\u6d4b\u4e00\u4e0b\u3002<\/p>\n\n\n\n

$ iqtree -s example.phy -symtest<\/strong><\/p>\n\n\n\n

2.0.3\u7248\u672c\u4e2d\u589e\u52a0\u4e86LSD2\u6cd5\u5bf9\u8fdb\u5316\u65f6\u95f4\u7684\u63a8\u7b97\u3002\u4e0d\u8fc7\u76ee\u524d\u6709\u4e24\u4e2a\u4e0d\u8db3\u4e4b\u5904\uff0c\u4e00\u662f\u7ed9\u51fa\u7684\u7ed3\u679c\u5c5e\u4e8e\u70b9\u4f30\u8ba1\uff0c\u4e8c\u662f\u5f53\u4e0d\u540c\u5e8f\u5217\u6216\u7269\u79cd\u95f4\u8fdb\u5316\u901f\u7387\u5dee\u5f02\u8f83\u5927\u65f6\uff0c\u53ef\u80fd\u4e0d\u592a\u7075\u5149\u3002<\/p>\n\n\n\n

\u4e09\u3001\u5c0f\u7ed3<\/strong><\/strong><\/h1>\n\n\n\n

\u65e2\u7136\u8bf4\u5230\u5efa\u6811\u57fa\u4e8e\u591a\u5e8f\u5217\u6bd4\u5bf9\uff0c\u5c31\u4e0d\u5f97\u4e0d\u4ecb\u7ecd\u4e00\u4e0b\u6574\u4f53\u6d41\u7a0b\uff1a<\/p>\n\n\n\n

\u2460\u6311\u9009\u5408\u9002\u7684\u57fa\u56e0\u751f\u6210fasta\u6587\u4ef6\uff08DNA\/AA\uff09<\/p>\n\n\n\n

\u2461\u591a\u5e8f\u5217\u6bd4\u5bf9 (Mafft\/ ClustalW)<\/p>\n\n\n\n

\u2462\u53bb\u6389\u6bd4\u5bf9\u4e2d\u7684gap (TrimAl)<\/p>\n\n\n\n

\u2463\u8f6c\u6362\u683c\u5f0f\uff0c\u751f\u6210\u7684FASTA, NEXUS, CLUSTALW\u683c\u5f0f\u7684\u6587\u4ef6\u5747<\/p>\n\n\n\n

\u2464\u5efa\u6811 (IQ-TREE)<\/p>\n\n\n\n

\u2465\u8fdb\u5316\u6811\u7f8e\u5316\uff08figtree\u3001itol\u3001mega\uff09<\/p>\n\n\n\n

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\"\"<\/figure>\n\n\n\n

\u56fe6 Mega\u8f6f\u4ef6\u53ef\u89c6\u5316\u8fdb\u5316\u6811<\/p>\n\n\n\n

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