{"id":1575,"date":"2025-06-09T20:27:05","date_gmt":"2025-06-09T12:27:05","guid":{"rendered":"http:\/\/www.majunpeng.com\/?p=1575"},"modified":"2025-06-09T21:20:06","modified_gmt":"2025-06-09T13:20:06","slug":"phyparts%e8%bf%9b%e8%a1%8c%e7%b3%bb%e7%bb%9f%e5%8f%91%e8%82%b2%e5%86%b2%e7%aa%81%e5%88%86%e6%9e%90","status":"publish","type":"post","link":"http:\/\/www.majunpeng.com\/index.php\/2025\/06\/09\/phyparts%e8%bf%9b%e8%a1%8c%e7%b3%bb%e7%bb%9f%e5%8f%91%e8%82%b2%e5%86%b2%e7%aa%81%e5%88%86%e6%9e%90\/","title":{"rendered":"Phyparts\u8fdb\u884c\u7cfb\u7edf\u53d1\u80b2\u51b2\u7a81\u5206\u6790"},"content":{"rendered":"\t\t<div data-elementor-type=\"wp-post\" data-elementor-id=\"1575\" class=\"elementor elementor-1575\" data-elementor-post-type=\"post\">\n\t\t\t\t<div class=\"elementor-element elementor-element-ca7639c e-flex e-con-boxed e-con e-parent\" data-id=\"ca7639c\" data-element_type=\"container\" data-e-type=\"container\">\n\t\t\t\t\t<div class=\"e-con-inner\">\n\t\t\t\t<div class=\"elementor-element elementor-element-b1d88db elementor-widget elementor-widget-heading\" data-id=\"b1d88db\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"heading.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t<h2 class=\"elementor-heading-title elementor-size-default\">1. \u524d\u8a00<\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-10fd59c elementor-widget elementor-widget-text-editor\" data-id=\"10fd59c\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t<p>\u6700\u8fd1\u53d7\u4e86\u8001\u5e08\u7684\u6307\u6d3e\uff0c\u5b66\u4e60\u7cfb\u7edf\u53d1\u80b2\u5206\u6790\u90e8\u5206\uff0c\u867d\u7136\u5927\u90e8\u5206\u7855\u58eb\u7684\u65f6\u5019\u90fd\u505a\u8fc7\uff0c\u4f46\u662f\u73b0\u5728\u770b\u6765\u6709\u4e9b\u5206\u6790\u786e\u5b9e\u53ef\u4ee5\u4f18\u5316\u4e00\u4e0b\u5417\u3002\u4eca\u5929\u5c31\u6765\u91cd\u65b0\u5b66\u4e60\u5e76\u4e14\u4f18\u5316\u4e00\u4e0b\u7cfb\u7edf\u53d1\u80b2\u51b2\u7a81\u5206\u6790\u3002\u8fd9\u6b21\u65b0\u5b66\u4e60\u7684\u65f6\u5019\u5f15\u5165\u4e86\u4e00\u4e2a\u65b0\u7684\u65b9\u6cd5\uff0c\u53ef\u4ee5\u901a\u8fc7\u5408\u5e76\u4e24\u6b21phyparts\u7684\u7ed3\u679c\uff0c\u5c06\u57fa\u56e0\u6811\u4e0a\u4e22\u5931\u548c\u4f4e\u4e8e\u652f\u6301\u7387\u7684\u5206\u652f\u8fdb\u4e00\u6b65\u7ec6\u5316\uff0c\u5e76\u4e14\u6839\u636e\u6bd4\u503c\u7ed8\u5236\u997c\u56fe\u3002<\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-4914332 elementor-widget elementor-widget-heading\" data-id=\"4914332\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"heading.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t<h2 class=\"elementor-heading-title elementor-size-default\">2. \u8f6f\u4ef6\u4e0b\u8f7d<\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-d087c99 elementor-widget elementor-widget-code-highlight\" data-id=\"d087c99\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"code-highlight.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<div class=\"prismjs-okaidia  \">\n\t\t\t<pre data-line=\"\" class=\"highlight-height language-bash line-numbers\">\n\t\t\t\t<code readonly=\"true\" class=\"language-bash\">\n\t\t\t\t\t<xmp>mamba create -n phyparts\nmamba activate phyparts\nmamba install conda-forge::maven\ngit clone https:\/\/gitee.com\/yen233\/phyparts.git\n.\/mvn_cmdline.sh\n\n\n<\/xmp>\n\t\t\t\t<\/code>\n\t\t\t<\/pre>\n\t\t<\/div>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-f586682 elementor-widget elementor-widget-heading\" data-id=\"f586682\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"heading.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t<h2 class=\"elementor-heading-title elementor-size-default\">3. \u8f93\u5165\u6587\u4ef6<\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-d889307 elementor-widget elementor-widget-text-editor\" data-id=\"d889307\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t<p>\u8f93\u5165\u6587\u4ef6\u5c31\u662f\u4e24\u4e2a\uff0c\uff081\uff09\u5355\u57fa\u56e0\u6811\uff0c\u8981\u6c42\u662f\u5e26\u6709\u652f\u6301\u7387\u5e76\u4e14\u5b9a\u6839\uff082\uff09\u7269\u79cd\u6811\uff0c\u540c\u6837\u8981\u6c42\u5b9a\u6839<\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-69cfb4a elementor-widget elementor-widget-heading\" data-id=\"69cfb4a\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"heading.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t<h2 class=\"elementor-heading-title elementor-size-default\">4. \u8fd0\u884c<\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-6b272c7 elementor-widget elementor-widget-code-highlight\" data-id=\"6b272c7\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"code-highlight.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<div class=\"prismjs-okaidia copy-to-clipboard \">\n\t\t\t<pre data-line=\"\" class=\"highlight-height language-python line-numbers\">\n\t\t\t\t<code readonly=\"true\" class=\"language-python\">\n\t\t\t\t\t<xmp>java -jar script\/target\/phyparts-0.0.1-SNAPSHOT-jar-with-dependencies.jar -a 1 -v -s 50 -d gene_trees -m RAxML_bestTree.tre -o mo\njava -jar \/mnt\/linxh\/software\/phyparts\/target\/phyparts-0.0.1-SNAPSHOT-jar-with-dependencies.jar -a 0 -v -d gene_trees -m RAxML_bestTree.tre.rooted.newick -o mo1\n\n# -a \u6a21\u5f0f\n# -s \u652f\u6301\u7387\u7684\u622a\u65ad\u503c\n# -d \u57fa\u56e0\u6811\n# -m \u7269\u79cd\u6811\n<\/xmp>\n\t\t\t\t<\/code>\n\t\t\t<\/pre>\n\t\t<\/div>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-09bac86 elementor-widget elementor-widget-text-editor\" data-id=\"09bac86\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t<p>\u4f7f\u7528R\u5c06\u4e24\u6b21\u7684\u7ed3\u679c\u5408\u5e76<\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-f396b82 elementor-widget elementor-widget-code-highlight\" data-id=\"f396b82\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"code-highlight.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<div class=\"prismjs-okaidia copy-to-clipboard \">\n\t\t\t<pre data-line=\"\" class=\"highlight-height language-bash line-numbers\">\n\t\t\t\t<code readonly=\"true\" class=\"language-bash\">\n\t\t\t\t\t<xmp>library(phytools)\r\n\r\nread.tree(\"A_0_No_BS_RT_all_homologs.concon.tre\")->No_bs #Tree file output from phyparts of concordance (-a 0) anlysis with out support filtering (-s)\r\nread.tree(\"A_1_BS_50_RT_all_homologs.concon.tre\")->bs_full_concordance #Tree file output from phyparts of full concordance anlysis (-a 1) with support filtering (e.g. Bootstrap 50; -s 50)\r\n\r\ntotal_no_bs<-No_bs[[1]] # get a tree to add total node numbers\r\n\r\ntotal_no_bs$node.label<-mapply(\"+\",as.numeric(No_bs[[1]]$node.label), as.numeric(No_bs[[2]]$node.label)) #get total number of nodes\r\ntotal_no_bs$node.label[is.na(total_no_bs$node.label)] <- \"\" #remove NA values\r\ntotal_no_bs$node.label[total_no_bs$node.label==\"0\"]<-\"\" #remove 0 values. to avoid divisions by zero.\r\n\r\n\r\nappend(bs_full_concordance, total_no_bs, after=2)-> full_concordance_and_total_nodes #append tree with total number of nodes to tree file output from phyparts of full concordance anlysis\r\n\r\nwrite.tree(full_concordance_and_total_nodes, file = \"A_1_BS_50_RT_all_homologs.concon.tre\") #write tree. this will replace to orignal file.\r\n<\/xmp>\n\t\t\t\t<\/code>\n\t\t\t<\/pre>\n\t\t<\/div>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-8540272 elementor-widget elementor-widget-heading\" data-id=\"8540272\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"heading.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t<h3 class=\"elementor-heading-title elementor-size-default\">\u53ef\u89c6\u5316\uff08\u5220\u9664\u7f3a\u5931\u7684\u7269\u79cd\uff09<\/h3>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-9e95660 elementor-widget elementor-widget-code-highlight\" data-id=\"9e95660\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"code-highlight.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<div class=\"prismjs-okaidia copy-to-clipboard \">\n\t\t\t<pre data-line=\"\" class=\"highlight-height language-bash line-numbers\">\n\t\t\t\t<code readonly=\"true\" class=\"language-bash\">\n\t\t\t\t\t<xmp>python \/mnt\/linxh\/software\/paralog_scripts\/phypartspiecharts_proportional.py RAxML_bestTree.tre.rooted.newick mo\n\n<\/xmp>\n\t\t\t\t<\/code>\n\t\t\t<\/pre>\n\t\t<\/div>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-2eb1e30 elementor-widget elementor-widget-image\" data-id=\"2eb1e30\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"image.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<img decoding=\"async\" src=\"https:\/\/bytebucket.org\/dfmoralesb\/target_enrichment_orthology\/raw\/b9dbb81bf759ca354b3fd6371b8bd51acefa8fbe\/images\/3_Proportional.png\" title=\"\" alt=\"\" loading=\"lazy\" \/>\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-9293975 elementor-widget elementor-widget-heading\" data-id=\"9293975\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"heading.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t<h3 class=\"elementor-heading-title elementor-size-default\">\u53ef\u89c6\u5316\uff08\u7f3a\u5931\u548c\u4f4e\u4e8e\u652f\u6301\u7387\u9608\u503c\u7528\u4e0d\u540c\u7684\u989c\u8272\u533a\u5206\uff09<\/h3>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-bd30481 elementor-widget elementor-widget-code-highlight\" data-id=\"bd30481\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"code-highlight.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<div class=\"prismjs-okaidia copy-to-clipboard \">\n\t\t\t<pre data-line=\"\" class=\"highlight-height language-javascript line-numbers\">\n\t\t\t\t<code readonly=\"true\" class=\"language-javascript\">\n\t\t\t\t\t<xmp>python \/mnt\/linxh\/software\/paralog_scripts\/phypartspiecharts_missing_uninformative.py RAxML_bestTree.tre.rooted.newick mo 538<\/xmp>\n\t\t\t\t<\/code>\n\t\t\t<\/pre>\n\t\t<\/div>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-b3dd8ac elementor-widget elementor-widget-image\" data-id=\"b3dd8ac\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"image.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<img decoding=\"async\" src=\"https:\/\/bytebucket.org\/dfmoralesb\/target_enrichment_orthology\/raw\/b9dbb81bf759ca354b3fd6371b8bd51acefa8fbe\/images\/2_Missing_and_uninfomtaive.png\" title=\"\" alt=\"\" loading=\"lazy\" \/>\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t","protected":false},"excerpt":{"rendered":"<p>1. \u524d\u8a00 \u6700\u8fd1\u53d7\u4e86\u8001\u5e08\u7684\u6307\u6d3e\uff0c\u5b66\u4e60\u7cfb\u7edf\u53d1\u80b2\u5206\u6790\u90e8\u5206\uff0c\u867d\u7136\u5927\u90e8\u5206\u7855\u58eb\u7684\u65f6\u5019\u90fd\u505a\u8fc7\uff0c\u4f46\u662f\u73b0\u5728\u770b\u6765\u6709\u4e9b\u5206\u6790\u786e\u5b9e\u53ef\u4ee5 &#8230; <a title=\"Phyparts\u8fdb\u884c\u7cfb\u7edf\u53d1\u80b2\u51b2\u7a81\u5206\u6790\" class=\"read-more\" href=\"http:\/\/www.majunpeng.com\/index.php\/2025\/06\/09\/phyparts%e8%bf%9b%e8%a1%8c%e7%b3%bb%e7%bb%9f%e5%8f%91%e8%82%b2%e5%86%b2%e7%aa%81%e5%88%86%e6%9e%90\/\" aria-label=\"\u9605\u8bfb Phyparts\u8fdb\u884c\u7cfb\u7edf\u53d1\u80b2\u51b2\u7a81\u5206\u6790\">\u9605\u8bfb\u66f4\u591a<\/a><\/p>\n","protected":false},"author":1,"featured_media":1577,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"_acf_changed":false,"_crdt_document":"","footnotes":""},"categories":[12],"tags":[],"class_list":["post-1575","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-12"],"acf":[],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v23.6 - https:\/\/yoast.com\/wordpress\/plugins\/seo\/ -->\n<title>Phyparts\u8fdb\u884c\u7cfb\u7edf\u53d1\u80b2\u51b2\u7a81\u5206\u6790 - \u5c0f\u9a6c\u751f\u4fe1\u65e5\u8bb0<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" 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