{"id":161,"date":"2021-11-22T23:01:57","date_gmt":"2021-11-22T15:01:57","guid":{"rendered":"https:\/\/linguopeng.top\/?p=161"},"modified":"2024-06-24T23:37:01","modified_gmt":"2024-06-24T15:37:01","slug":"%e7%89%b9%e5%bc%82%e5%9f%ba%e5%9b%a0-orthofinder","status":"publish","type":"post","link":"https:\/\/linguopeng.top\/?p=161","title":{"rendered":"\u7279\u5f02\u57fa\u56e0-OrthoFinder"},"content":{"rendered":"\n<pre class=\"wp-block-code\"><code>#\u524d\u8a00\uff1a\n##OrthoMCL (&#91;http:\/\/orthomcl.org\/orthomcl\/](https:\/\/links.jianshu.com\/go?to=http%3A%2F%2Forthomcl.org%2Forthomcl%2F)) \u662f\u73b0\u5728\u7528\u7684\u6700\u591a\u7684\u4e00\u6b3e\u6765\u627e\u76f4\u7cfb\u540c\u6e90\u57fa\u56e0\uff08Orthologs\uff09\u4ee5\u53ca\u65c1\u7cfb\u540c\u6e90\u57fa\u56e0 (Paralog) \u7684\u8f6f\u4ef6 \uff0c\u540c\u6e90\u57fa\u56e0\u7684\u5b9a\u4f4d\u548c\u6ce8\u91ca\u5728\u5bf9\u57fa\u56e0\u7ec4\u540e\u7eed\u5206\u6790\u4e2d\u81f3\u5173\u91cd\u8981\u3002\u5b83\u4e3b\u8981\u5728\u6bd4\u8f83\u5b8c\u6574\u7684\u57fa\u56e0\u7ec4\u4e4b\u95f4\u627e\u76f4\u7cfb\u540c\u6e90\u57fa\u56e0\u3002OrthoMCL\u7684\u4f7f\u7528\u4e3b\u8981\u670913\u6b65\uff0c\u5b98\u65b9\u5728**2013\u5e74\u516c\u5e03OrthoMCL v2.0**\u7248\u672c\u5c31\u5f88\u4e45\u6ca1\u6709\u66f4\u65b0\u8fc7\u3002\u4ecev1.4\u6700\u521d\u7248\u672c\u8bf4\u660e\u6587\u6863\u53ef\u4ee5\u4e86\u89e3OrthoMCL\u7684\u4f7f\u7528\u6b65\u9aa4\uff0c\u5927\u4f53\u6709Mysql\u6570\u636e\u5e93\u914d\u7f6e\u3001\u4fee\u6539OrthoMCL\u914d\u7f6e\u6587\u4ef6\u3001\u8f6c\u6362\u5e8f\u5217\u683c\u5f0f\u3001\u8fc7\u6ee4\u3001\u6bd4\u5bf9\u3001\u89e3\u6790\u7ed3\u679c\u548c\u805a\u7c7b\u7b49\u6b65\u9aa4\uff0c\u7279\u522b\u9ebb\u70e6\u3002\u5e76\u4e14\u7531\u4e8eMySql\u6570\u636e\u5e93\u7684\u5b89\u88c5\u548c\u914d\u7f6e\u7684\u8fc7\u7a0b\u4e5f\u9700\u8981\u7ba1\u7406\u5458\u6743\u9650\u3002\n##OrthoFinder\uff08&#91;\u6587\u7ae0\u94fe\u63a5](https:\/\/links.jianshu.com\/go?to=https%3A%2F%2Fgenomebiology.biomedcentral.com%2Farticles%2F10.1186%2Fs13059-015-0721-2)\uff09\u540c\u6837\u662f\u5bfb\u627e\u540c\u6e90\u57fa\u56e0\u7684\u5229\u5668\uff0c\u4f18\u52bf\u5728\u4e8e\u7248\u672c\u8f83\u65b0\uff0c\u5e94\u7528\u65b9\u4fbf,\n#Emms, D.M. and Kelly, S. **(2019**) OrthoFinder: phylogenetic orthology inference for comparative genomics. Genome Biology 20:238\n#Emms, D.M. and Kelly, S. (**2015**) OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy. Genome Biology 16:157\u76f8\u5173\u4ecb\u7ecd\u53ef\u5728&#91;github\u67e5\u770b]<\/code><\/pre>\n\n\n\n<figure class=\"wp-block-image size-large\"><div class='fancybox-wrapper lazyload-container-unload' data-fancybox='post-images' href='https:\/\/linguopeng.top\/wp-content\/uploads\/2021\/11\/orthofinder.png'><img class=\"lazyload lazyload-style-1\" src=\"data:image\/svg+xml;base64,PCEtLUFyZ29uTG9hZGluZy0tPgo8c3ZnIHdpZHRoPSIxIiBoZWlnaHQ9IjEiIHhtbG5zPSJodHRwOi8vd3d3LnczLm9yZy8yMDAwL3N2ZyIgc3Ryb2tlPSIjZmZmZmZmMDAiPjxnPjwvZz4KPC9zdmc+\"  decoding=\"async\" data-original=\"https:\/\/linguopeng.top\/wp-content\/uploads\/2021\/11\/orthofinder.png\" src=\"data:image\/png;base64,iVBORw0KGgoAAAANSUhEUgAAAAEAAAABCAYAAAAfFcSJAAAAAXNSR0IArs4c6QAAAARnQU1BAACxjwv8YQUAAAAJcEhZcwAADsQAAA7EAZUrDhsAAAANSURBVBhXYzh8+PB\/AAffA0nNPuCLAAAAAElFTkSuQmCC\" alt=\"\"\/><\/div><\/figure>\n\n\n\n<pre class=\"wp-block-code\"><code>#\u5b89\u88c5singularity,conda\u53ef\u5b89\u88c5\nconda env list\nconda activate singularity\n#\u628a\u6570\u636e\u653e\u7f6e\u5728\u4ee5\u4e0b\u76ee\u5f55\u4e2d\ncd ~\/PART\/PART3_Comparative_genomics\/PART3_Comparative_genomics\/01.GeneFamilyCluster\/data\/<\/code><\/pre>\n\n\n\n<figure class=\"wp-block-image size-large\"><div class='fancybox-wrapper lazyload-container-unload' data-fancybox='post-images' href='https:\/\/linguopeng.top\/wp-content\/uploads\/2021\/11\/-1536x741.png'><img class=\"lazyload lazyload-style-1\" src=\"data:image\/svg+xml;base64,PCEtLUFyZ29uTG9hZGluZy0tPgo8c3ZnIHdpZHRoPSIxIiBoZWlnaHQ9IjEiIHhtbG5zPSJodHRwOi8vd3d3LnczLm9yZy8yMDAwL3N2ZyIgc3Ryb2tlPSIjZmZmZmZmMDAiPjxnPjwvZz4KPC9zdmc+\"  decoding=\"async\" data-original=\"https:\/\/linguopeng.top\/wp-content\/uploads\/2021\/11\/-1536x741.png\" src=\"data:image\/png;base64,iVBORw0KGgoAAAANSUhEUgAAAAEAAAABCAYAAAAfFcSJAAAAAXNSR0IArs4c6QAAAARnQU1BAACxjwv8YQUAAAAJcEhZcwAADsQAAA7EAZUrDhsAAAANSURBVBhXYzh8+PB\/AAffA0nNPuCLAAAAAElFTkSuQmCC\" alt=\"\"\/><\/div><\/figure>\n\n\n\n<pre class=\"wp-block-code\"><code>#\u8fd4\u56de\u4e0a\u4e00\u5c42\u76ee\u5f55\ncd .. \n#\u6267\u884c\u811a\u672c\nnohup singularity  exec  ..\/software\/PhyloTools.sif orthofinder  -f data \\\n\t-S diamond \\\n\t-M msa \\\n\t-T fasttree \\\n\t-t 45 &amp;\n#\u8fd0\u884c\u7ed3\u679c\u4f1a\u4fdd\u5b58\u5728\u4e0a\u9762data\/OrthoFinder\uff0c\u4ee5\u65e5\u671f\u4e3a\u4fdd\u5b58\n#\u5728\u7ed3\u679c\u6587\u4ef6\u627e\u5230\u4e00\u4e0bOrthogroups_UnassignedGenes.tsv<\/code><\/pre>\n\n\n\n<figure class=\"wp-block-image size-large\"><div class='fancybox-wrapper lazyload-container-unload' data-fancybox='post-images' href='https:\/\/linguopeng.top\/wp-content\/uploads\/2021\/11\/2.png'><img class=\"lazyload lazyload-style-1\" src=\"data:image\/svg+xml;base64,PCEtLUFyZ29uTG9hZGluZy0tPgo8c3ZnIHdpZHRoPSIxIiBoZWlnaHQ9IjEiIHhtbG5zPSJodHRwOi8vd3d3LnczLm9yZy8yMDAwL3N2ZyIgc3Ryb2tlPSIjZmZmZmZmMDAiPjxnPjwvZz4KPC9zdmc+\"  decoding=\"async\" data-original=\"https:\/\/linguopeng.top\/wp-content\/uploads\/2021\/11\/2.png\" src=\"data:image\/png;base64,iVBORw0KGgoAAAANSUhEUgAAAAEAAAABCAYAAAAfFcSJAAAAAXNSR0IArs4c6QAAAARnQU1BAACxjwv8YQUAAAAJcEhZcwAADsQAAA7EAZUrDhsAAAANSURBVBhXYzh8+PB\/AAffA0nNPuCLAAAAAElFTkSuQmCC\" alt=\"\"\/><\/div><\/figure>\n\n\n\n<pre class=\"wp-block-code\"><code>#\u9000\u51fa\u73af\u5883\nconda activate\n#\u67e5\u770b\u7279\u5f02\u57fa\u56e0\u7684ID<\/code><\/pre>\n\n\n\n<pre class=\"wp-block-code\"><code>#\u6839\u636e\u9700\u8981\u7684\u83cc\u682a\u53e6\u5efa\u6587\u4ef6\u5939\uff0c\u4f8b\u5982\u5728\u6587\u4ef6\u5939\u91cc\u653e\u7f6eFAHBZ9L5\ncat FAHBZ9L5_CDS.fnn| seqkit grep -f list &gt; new.fa\n#new.fa\u4e3a\u4fdd\u5b58\u7684\u7279\u5f02\u57fa\u56e0\u7684\u6838\u9178\u5e8f\u5217\n#\u7528new.fa\u5230NCBI\u7684https:\/\/blast.ncbi.nlm.nih.gov\/\u8fdb\u4e00\u6b65\u7b5b\u9009\n#\u6700\u7ec8\u5448\u73b0\u4ee5\u4e0b\u56fe\u8868\u4e3a\u83cc\u682a\u7684\u57fa\u56e0\u5728NCBI\u641c\u7d22\u4e0d\u5230\uff0c\u8868\u660e\u4e3a\u7279\u5f02<\/code><\/pre>\n\n\n\n<figure class=\"wp-block-image size-full\"><div class='fancybox-wrapper lazyload-container-unload' data-fancybox='post-images' href='https:\/\/linguopeng.top\/wp-content\/uploads\/2021\/11\/NCBI.png'><img class=\"lazyload lazyload-style-1\" src=\"data:image\/svg+xml;base64,PCEtLUFyZ29uTG9hZGluZy0tPgo8c3ZnIHdpZHRoPSIxIiBoZWlnaHQ9IjEiIHhtbG5zPSJodHRwOi8vd3d3LnczLm9yZy8yMDAwL3N2ZyIgc3Ryb2tlPSIjZmZmZmZmMDAiPjxnPjwvZz4KPC9zdmc+\"  loading=\"lazy\" decoding=\"async\" width=\"654\" height=\"533\" data-original=\"https:\/\/linguopeng.top\/wp-content\/uploads\/2021\/11\/NCBI.png\" src=\"data:image\/png;base64,iVBORw0KGgoAAAANSUhEUgAAAAEAAAABCAYAAAAfFcSJAAAAAXNSR0IArs4c6QAAAARnQU1BAACxjwv8YQUAAAAJcEhZcwAADsQAAA7EAZUrDhsAAAANSURBVBhXYzh8+PB\/AAffA0nNPuCLAAAAAElFTkSuQmCC\" alt=\"\" class=\"wp-image-166\"\/><\/div><\/figure>\n","protected":false},"excerpt":{"rendered":"","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[1],"tags":[12],"class_list":["post-161","post","type-post","status-publish","format-standard","hentry","category-uncategorized","tag-linux"],"_links":{"self":[{"href":"https:\/\/linguopeng.top\/index.php?rest_route=\/wp\/v2\/posts\/161","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/linguopeng.top\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/linguopeng.top\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/linguopeng.top\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/linguopeng.top\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=161"}],"version-history":[{"count":4,"href":"https:\/\/linguopeng.top\/index.php?rest_route=\/wp\/v2\/posts\/161\/revisions"}],"predecessor-version":[{"id":661,"href":"https:\/\/linguopeng.top\/index.php?rest_route=\/wp\/v2\/posts\/161\/revisions\/661"}],"wp:attachment":[{"href":"https:\/\/linguopeng.top\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=161"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/linguopeng.top\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=161"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/linguopeng.top\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=161"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}