{"id":2213,"date":"2014-07-07T16:31:46","date_gmt":"2014-07-07T08:31:46","guid":{"rendered":"http:\/\/www.chenlianfu.com\/?p=2213"},"modified":"2014-07-07T16:31:46","modified_gmt":"2014-07-07T08:31:46","slug":"%e4%bd%bf%e7%94%a8-gblocks-%e6%8f%90%e5%8f%96%e4%bf%9d%e5%ae%88%e5%ba%8f%e5%88%97","status":"publish","type":"post","link":"http:\/\/www.chenlianfu.com\/?p=2213","title":{"rendered":"\u4f7f\u7528 Gblocks \u63d0\u53d6\u4fdd\u5b88\u5e8f\u5217"},"content":{"rendered":"<h1>1. Gblocks \u7b80\u4ecb<\/h1>\n<p>Gblocks\u7528\u4e8e\u4ece\u591a\u5e8f\u5217\u6bd4\u5bf9\u7ed3\u679c\u4e2d\u63d0\u53d6\u4fdd\u5b88\u4f4d\u70b9\uff0c\u4ee5\u5229\u4e8e\u4e0b\u4e00\u6b65\u7684\u8fdb\u5316\u5206\u6790\u3002<br \/>\n\u5728\u7ebf\u8bf4\u660e\u6587\u6863\uff1a<a href=\"http:\/\/molevol.cmima.csic.es\/castresana\/Gblocks\/Gblocks_documentation.html\" target=\"_blank\">http:\/\/molevol.cmima.csic.es\/castresana\/Gblocks\/Gblocks_documentation.html<\/a><br \/>\n\u5728\u7ebf\u670d\u52a1\u7f51\u7ad9\uff1a<a href=\"http:\/\/molevol.cmima.csic.es\/castresana\/Gblocks_server.html\" target=\"_blank\">http:\/\/molevol.cmima.csic.es\/castresana\/Gblocks_server.html<\/a><\/p>\n<h1>2. Gblocks \u5b89\u88c5<\/h1>\n<pre>\r\n$ wget http:\/\/molevol.cmima.csic.es\/castresana\/Gblocks\/Gblocks_Linux64_0.91b.tar.Z\r\n$ sudo yum install -y ncompress\r\n$ tar Zxf Gblocks_Linux64_0.91b.tar.Z -C \/opt\/biosoft\/\r\n$ echo 'PATH=$PATH:\/opt\/biosoft\/Gblocks_0.91b\/' >> ~\/.bashrc\r\n$ source ~\/.bashrc\r\n<\/pre>\n<h1>3. Gblocks \u4f7f\u7528<\/h1>\n<p>Gblosk \u6709\u4e24\u79cd\u4f7f\u7528\u65b9\u5f0f\uff0c\u7b2c\u4e00\u79cd\u662f\u4ea4\u4e92\u5f0f\u7684\u65b9\u5f0f\uff08\u6309\u63d0\u793a\u8f93\u5165\u6587\u4ef6\u6539\u53d8\u53c2\u6570\uff09\uff0c\u7b2c\u4e8c\u79cd\u662f\u547d\u4ee4\u884c\u5f0f\uff08\u5728\u547d\u4ee4\u884c\u4e2d\u8f93\u5165\u53c2\u6570\uff09\u3002<br \/>\n\u547d\u4ee4\u884c\u5f0f\u7684\u5e38\u7528\u4f8b\u5b50\uff1a<\/p>\n<pre>\r\n\u4f7f\u7528\u9ed8\u8ba4\u7684\u8bbe\u7f6e\uff1a\r\n$ Gblocks proteins.fasta -t=p\r\n\u5fc5\u987b\u662f fasta \u6587\u4ef6\u5728\u524d\uff0c\u53c2\u6570\u5728\u540e\u3002\u82e5\u6ca1\u6709\u53c2\u6570\uff0c\u5219\u8fdb\u5165\u4ea4\u4e92\u5f0f\u754c\u9762\u3002\r\n\r\n\u5f97\u5230\u66f4\u957f\u7684\u5e8f\u5217\uff1a\r\n$ Gblocks proteins.fasta -b4=5 -b5=h\r\n<\/pre>\n<p>\u547d\u4ee4\u884c\u5f0f\u7684\u5e38\u7528\u53c2\u6570\uff1a<\/p>\n<pre>\r\n-t= default:p\r\n\u8bbe\u7f6e\u5e8f\u5217\u7684\u7c7b\u578b\uff0c\u53ef\u9009\u7684\u503c\u662f p,d,c \u5206\u522b\u4ee3\u8868 protein\uff0c DNA\uff0c Codons \u3002\r\n-b1= default:\uff08 \u5e8f\u5217\u6761\u6570\u7684 50% + 1 \uff09\r\n\u8bbe\u5b9a\u4fdd\u5b88\u6027\u4f4d\u70b9\u5fc5\u987b\u6709 >= \u8be5\u503c\u7684\u5e8f\u5217\u6570\u3002\u8be5\u53c2\u6570\u540e\u63a5\u4e00\u4e2a integer \u6570\uff0c\u9ed8\u8ba4\u4e0b\u6bd4\u5e8f\u5217\u6761\u6570\u7684 50% \u5927 1.\r\n-b2= default: \u5e8f\u5217\u6761\u6570\u7684 85%\r\n\u786e\u5b9a\u4fdd\u5b88\u4f4d\u70b9\u7684\u4fa7\u7ffc\u4f4d\u70b9\u65f6\uff0c\u5176\u4f4d\u70b9\u5fc5\u987b\u6709 >= \u8be5\u503c\u7684\u5e8f\u5217\u6570\u3002\u8be5\u503c\u5fc5\u987b\u8981\u6bd4 -b1 \u7684\u503c\u8981\u5927\u3002\r\n-b3= default: 8\r\n\u6700\u5927\u8fde\u7eed\u975e\u4fdd\u5b88\u4f4d\u70b9\u7684\u957f\u5ea6\u3002\r\n-b4= default: 10\r\n\u4fdd\u5b88\u4f4d\u70b9\u533a\u5757\u7684\u6700\u5c0f\u957f\u5ea6\u3002\u8be5\u503c\u5fc5\u987b >=2 \u3002\r\n-b5= default: n\r\n\u8bbe\u7f6e\u5141\u8bb8\u542b\u6709 Gap \u4f4d\u70b9\u3002\u53ef\u9009\u7684\u503c\u6709 n,h,a \u5206\u522b\u4ee3\u8868 None, With Half, All \u3002 \u5f53\u4e3a h \u65f6\uff0c\u8868\u793a\r\n-e= default: -gb\r\n\u8bbe\u7f6e\u8f93\u51fa\u7ed3\u679c\u7684\u540e\u7f00\u3002\r\n<\/pre>\n","protected":false},"excerpt":{"rendered":"<p>1. Gblocks \u7b80\u4ecb Gblocks\u7528\u4e8e\u4ece\u591a\u5e8f\u5217\u6bd4\u5bf9\u7ed3\u679c\u4e2d\u63d0\u53d6\u4fdd\u5b88\u4f4d\u70b9\uff0c\u4ee5 &hellip; <a href=\"http:\/\/www.chenlianfu.com\/?p=2213\">\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\/2213"}],"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=2213"}],"version-history":[{"count":1,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2213\/revisions"}],"predecessor-version":[{"id":2216,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2213\/revisions\/2216"}],"wp:attachment":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=2213"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=2213"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=2213"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}