{"id":2225,"date":"2014-07-08T13:36:55","date_gmt":"2014-07-08T05:36:55","guid":{"rendered":"http:\/\/www.chenlianfu.com\/?p=2225"},"modified":"2019-04-17T23:39:30","modified_gmt":"2019-04-17T15:39:30","slug":"%e4%bd%bf%e7%94%a8-raxml-%e6%9e%84%e5%bb%ba%e8%bf%9b%e5%8c%96%e6%a0%91","status":"publish","type":"post","link":"http:\/\/www.chenlianfu.com\/?p=2225","title":{"rendered":"\u4f7f\u7528 RAxML \u6784\u5efa\u8fdb\u5316\u6811"},"content":{"rendered":"<h1>1. RAxML \u7b80\u4ecb<\/h1>\n<p>RAxML (Random Axelerated Maximum Likelikhood) \u80fd\u4f7f\u7528\u591a\u7ebf\u7a0b\u6216\u5e76\u884c\u5316\u4f7f\u7528\u6700\u5927\u4f3c\u7136\u6cd5\u6784\u5efa\u8fdb\u5316\u6811\u3002<br \/>\n\u7f51\u9875\u7248\u5de5\u5177\uff1a<a href=\"http:\/\/epa.h-its.org\/raxml\/submit_single_gene\" target=\"_blank\" rel=\"noopener noreferrer\">http:\/\/epa.h-its.org\/raxml\/submit_single_gene<\/a><br \/>\n\u53c2\u8003\u6587\u732e\uff1a<a href=\"http:\/\/bioinformatics.oxfordjournals.org\/content\/30\/9\/1312.full\" target=\"_blank\" rel=\"noopener noreferrer\">RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies<\/a><\/p>\n<h1>2. RAxML \u4e0b\u8f7d\u4e0e\u5b89\u88c5<\/h1>\n<pre>$ wget https:\/\/github.com\/stamatak\/standard-RAxML\/archive\/v8.2.12.tar.gz -O ~\/software\/RAxML-v8.2.12.tar.gz\n$ tar zxf ~\/software\/RAxML-v8.2.12.tar.gz -C \/opt\/biosoft\/\n$ mv \/opt\/biosoft\/standard-RAxML-8.2.12\/ \/opt\/biosoft\/RAxML-8.2.12\/\n$ cd \/opt\/biosoft\/RAxML-8.2.12\/\n$ make -f Makefile.SSE3.PTHREADS.gcc -j 4\n$ rm *.o\n$ make -f Makefile.AVX.PTHREADS.gcc -j 4\n$ rm *.o\n$ source ~\/.bashrc.mpich\n$ make -f Makefile.SSE3.HYBRID.gcc -j 4\n$ rm *.o\n$ make -f Makefile.AVX.HYBRID.gcc -j 4\n$ rm *.o\n$ chmod 755 \/opt\/biosoft\/RAxML-8.2.12\/usefulScripts\/*\n$ echo 'PATH=$PATH:\/opt\/biosoft\/RAxML-8.2.12\/' &gt;&gt; ~\/.bashrc\n$ source ~\/.bashrc<\/pre>\n<h1>2. RAxML \u7684\u4f7f\u7528<\/h1>\n<p>RaxML \u8f6f\u4ef6\u5305\u4e2d\u5e26\u6709\u4e00\u4e2a PDF \u683c\u5f0f\u7684 Manual \u6587\u6863\uff0c\u4ecb\u7ecd\u5f97\u975e\u5e38\u8be6\u7ec6\u3002<\/p>\n<h2>2.1 RaxML \u7248\u672c\u7684\u9009\u62e9<\/h2>\n<p>Sequential \u7248\u672c\u9002\u5408\u4e8e\u4e2d\u5c0f\u578b\u7684\u6570\u636e\uff1b PThreads \u7248\u672c\u9002\u5408\u4e8e\u957f\u5e8f\u5217\u6216\u591a\u6761\u5e8f\u5217\uff1bMPI \u7248\u672c\u9002\u5408\u4e8e\u8f83\u5927(100~1000) bootstraps \u7684\u8fd0\u884c\u3002<\/p>\n<h2>2.2 \u5e38\u7528\u4f8b\u5b50\u4e0e\u53c2\u6570<\/h2>\n<p>\u5e38\u7528\u4f8b\u5b50\uff1a<\/p>\n<pre>\u7b80\u5355\u5feb\u901f\u65b9\u5f0f\n$ raxmlHPC \u00ad-f a \u00ad-x 12345 \u00ad-p 12345 \u00ad-# 100 \u00ad-m PROTGAMMALGX \u00ad-s ex.phy \u00ad-n ex -T 20\n\n\u5e76\u884c\u5316\u8f6f\u4ef6\u652f\u6301\uff0c\u80fd\u6700\u5feb\u901f\u8ba1\u7b97\u3002\u5e76\u884c\u531620\u4e2a\u4efb\u52a1\uff0c\u6bcf\u4e2a\u4efb\u52a1\u4f7f\u75288\u7ebf\u7a0b\uff0c\u80fd\u4f7f\u7528\u5168\u90e8160\u7ebf\u7a0b\u8ba1\u7b97\u8d44\u6e90\uff1a\n$ \/opt\/sysoft\/mpich2-1.5\/bin\/mpirun -np 20 raxmlHPC \u00ad-f a \u00ad-x 12345 \u00ad-p 12345 \u00ad-# 100 \u00ad-m PROTGAMMALGX \u00ad-s ex.phy \u00ad-n ex -T 8<\/pre>\n<p>RAxML \u7684\u53c2\u6570\u975e\u5e38\u591a\uff0c\u8bbe\u7f6e\u975e\u5e38\u590d\u6742\uff0c\u4e0a\u8ff0\u5e38\u7528\u4f8b\u5b50\u7684\u53c2\u6570\u4e3a\uff1a<\/p>\n<pre>-f a\n\u6b64\u53c2\u6570\u7528\u4e8e\u9009\u62e9 RAxML \u8fd0\u7b97\u7684\u7b97\u6cd5\u3002\u53ef\u4ee5\u8bbe\u5b9a\u7684\u503c\u975e\u5e38\u4e4b\u591a\u3002 a \u8868\u793a\u6267\u884c\u5feb\u901f Bootstrap \u5206\u6790\u5e76\u641c\u7d22\u6700\u4f73\u5f97\u5206\u7684 ML \u6811\u3002\n-x 12345\n\u6307\u5b9a\u4e00\u4e2a int \u6570\u4f5c\u4e3a\u968f\u673a\u79cd\u5b50\uff0c\u4ee5\u542f\u7528\u5feb\u901f Bootstrap \u7b97\u6cd5\u3002\n-p 12345\n\u6307\u5b9a\u4e00\u4e2a\u968f\u673a\u6570\u4f5c\u4e3a parsimony inferences \u7684\u79cd\u5b50\u3002\n-# 100\n\u6307\u5b9a bootstrap \u7684\u6b21\u6570\u3002\n-m PROTGAMMALGX\n\u6307\u5b9a\u6838\u82f7\u9178\u6216\u6c28\u57fa\u9178\u66ff\u4ee3\u6a21\u578b\u3002PROTGAMMALGX \u7684\u89e3\u91ca\uff1a \"PROT\" \u8868\u793a\u6c28\u57fa\u9178\u66ff\u4ee3\u6a21\u578b\uff1b GAMMA \u8868\u793a\u4f7f\u7528 GAMMA \u6a21\u578b\uff1b X \u8868\u793a\u4f7f\u7528\u6700\u5927\u4f3c\u7136\u6cd5\u4f30\u8ba1\u78b1\u57fa\u9891\u7387\u3002\n-s ex.phy\n\u6307\u5b9a\u8f93\u5165\u6587\u4ef6\u3002phy \u683c\u5f0f\u7684\u591a\u5e8f\u5217\u6bd4\u5bf9\u7ed3\u679c\u3002\u8f6f\u4ef6\u5305\u4e2d\u5305\u542b\u4e00\u4e2a\u7a0b\u5e8f\u6765\u5c06 fasta \u683c\u5f0f\u8f6c\u6362\u4e3a phy \u683c\u5f0f\u3002\n-n ex\n\u8f93\u51fa\u6587\u4ef6\u7684\u540e\u7f00\u4e3a .ex \u3002\n-T 20\n\u6307\u5b9a\u591a\u7ebf\u7a0b\u8fd0\u884c\u7684 CPUs \u3002\n<\/pre>\n<h2>2.3 \u7ed3\u679c\u6587\u4ef6<\/h2>\n<pre>RAxML_bootstrap.ex           bootstrapped trees\nRAxML_bestTree.ex            \u6700\u4f73\u5f97\u5206 ML \u6811\nRAxML_bipartitions.ex        \u6709 bootstrap \u5206\u503c\u652f\u6301\u7684\u6700\u4f73\u5f97\u5206\u6811\uff0c\u5206\u503c\u5728 node \u4e0a\u3002\nRAxML_bipartionsBranchLabels.ex \u6709 bootstrap \u5206\u503c\u652f\u6301\u7684\u6700\u4f73\u5f97\u5206\u6811, \u5206\u503c\u5728 branch \u4e0a\u3002FigTree\u4e0d\u80fd\u8bc6\u522b\u6b64\u6587\u4ef6\u3002\n<\/pre>\n","protected":false},"excerpt":{"rendered":"<p>1. RAxML \u7b80\u4ecb RAxML (Random Axelerated Max &hellip; <a href=\"http:\/\/www.chenlianfu.com\/?p=2225\">\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\/2225"}],"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=2225"}],"version-history":[{"count":5,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2225\/revisions"}],"predecessor-version":[{"id":2869,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2225\/revisions\/2869"}],"wp:attachment":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=2225"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=2225"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=2225"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}