{"id":2289,"date":"2025-10-20T19:24:02","date_gmt":"2025-10-20T11:24:02","guid":{"rendered":"http:\/\/www.majunpeng.com\/?p=2289"},"modified":"2025-10-28T20:05:35","modified_gmt":"2025-10-28T12:05:35","slug":"%e5%a4%9a%e5%80%8d%e5%8c%96%e5%88%86%e6%9e%90%e8%bd%af%e4%bb%b6%e7%9a%84%e7%9a%84%e5%8f%a6%e4%b8%80%e4%b8%aa%e9%80%89%e6%8b%a9wgd-v2","status":"publish","type":"post","link":"http:\/\/www.majunpeng.com\/index.php\/2025\/10\/20\/%e5%a4%9a%e5%80%8d%e5%8c%96%e5%88%86%e6%9e%90%e8%bd%af%e4%bb%b6%e7%9a%84%e7%9a%84%e5%8f%a6%e4%b8%80%e4%b8%aa%e9%80%89%e6%8b%a9wgd-v2\/","title":{"rendered":"\u591a\u500d\u5316\u5206\u6790\u8f6f\u4ef6\u7684\u7684\u53e6\u4e00\u4e2a\u9009\u62e9\u201cWGD V2\u201d"},"content":{"rendered":"\t\t<div data-elementor-type=\"wp-post\" data-elementor-id=\"2289\" class=\"elementor elementor-2289\" data-elementor-post-type=\"post\">\n\t\t\t\t<div class=\"elementor-element elementor-element-c4914a8 e-flex e-con-boxed e-con e-parent\" data-id=\"c4914a8\" 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-3b402a4 elementor-widget elementor-widget-heading\" data-id=\"3b402a4\" 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-c2dd397 elementor-widget elementor-widget-text-editor\" data-id=\"c2dd397\" 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>\u63d0\u8d77\u591a\u500d\u5316\uff08WGD\uff09\u5206\u6790\u8f6f\u4ef6\uff0c\u5927\u5bb6\u7b2c\u4e00\u65f6\u95f4\u60f3\u5230\u7684\u90fd\u662fWGDI\uff0c\u4f46\u662f\u5176\u5b9e\u8fd8\u6709\u53e6\u5916\u4e00\u6b3e\u8f6f\u4ef6\u4e5f\u80fd\u505a\u591a\u500d\u5316\uff0c\u76f8\u6bd4\u4e8eWGDI\uff0cWGD\u8fd9\u4e2a\u8f6f\u4ef6\u5bf9\u4e8eKs\u7684\u5cf0\u503c\u7684\u62df\u5408\u66f4\u52a0\u4e25\u683c\uff0c\u5e76\u4e14\u53ef\u4ee5\u5f97\u51fa\u591a\u500d\u5316\u7684\u65f6\u95f4\uff0c\u56e0\u6b64\u4eca\u5929\u5c31\u53ea\u7528WGD V2\u6765\u8ba1\u7b97\u591a\u500d\u5316\u7684\u65f6\u95f4\u3002\u8865\u5145\u4e00\u4e0b\uff0cWGD\u8f6f\u4ef6\u867d\u7136\u53ef\u4ee5\u8fdb\u884c\u591a\u500d\u5316\u5206\u6790\uff0c\u4f46\u662f\u5f88\u9ebb\u70e6\uff0c\u8981\u4e00\u6b21\u8fd0\u884c\u6bcf\u4e2a\u6a21\u5757\u3002<strong><span style=\"color: #ff0000;\">Ksrates\u8fd9\u4e2a\u8f6f\u4ef6\u96c6\u6210\u4e86WGD\u8f6f\u4ef6\u505a\u6240\u6709\u591a\u500d\u5316\u5206\u6790\u7684\u6d41\u7a0b\uff0c\u76f4\u63a5\u5c31\u80fd\u5b8c\u6210\u5206\u6790\u3002\u6240\u4ee5\u672c\u6559\u7a0b\u7684\u591a\u500d\u5316\u5206\u6790\u4f7f\u7528Ksrates\uff0c\u591a\u500d\u5316\u65f6\u95f4\u8bc4\u4f30\u8fd8\u662f\u4f7f\u7528WGD\u3002<\/span><\/strong><\/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-a20dd5c elementor-widget elementor-widget-heading\" data-id=\"a20dd5c\" 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-5e7874d elementor-widget elementor-widget-code-highlight\" data-id=\"5e7874d\" 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>mamba create -n wgd python==3.6.5\nmamba activate wgd\npip install numpy==1.19.0 -i https:\/\/pypi.tuna.tsinghua.edu.cn\/simple\npip install wgd==2.0.38 -i https:\/\/pypi.tuna.tsinghua.edu.cn\/simple\nmamba install bioconda::mcl\nmamba install bioconda::mafft\nmamba install bioconda::fasttree<\/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-0f9097d elementor-widget elementor-widget-heading\" data-id=\"0f9097d\" 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. \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-326ddbf elementor-widget elementor-widget-heading\" data-id=\"326ddbf\" 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\">3.1 Ksrates<\/h3>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-638300f elementor-widget elementor-widget-text-editor\" data-id=\"638300f\" 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>Ksrates\u548c\u4e00\u4e2a\u57fa\u4e8enextflow\u7684\u5de5\u4f5c\u6d41\uff0c\u8bf7\u81ea\u884c\u4e0b\u8f7dnextflow\u3002\u8fd0\u884c\u524d\u8981\u51c6\u59072\u4e2a\u914d\u7f6e\u6587\u4ef6\uff0cconfig_elaeis.txt\u548cconfig_expert.txt\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-ff81331 elementor-widget elementor-widget-code-highlight\" data-id=\"ff81331\" 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>head config_elaeis.txt\n\n[SPECIES]\nfocal_species = Prped\n# \u6307\u5b9a\u4e00\u4e2a\u7126\u70b9\u7269\u79cd\uff0c\u7126\u70b9\u7269\u79cd\u4f1a\u505a\u79cd\u5185\u7684Ks\u5206\u5e03\u548c\u5176\u4ed6\u7269\u79cd\u4e8e\u7126\u70b9\u7269\u79cd\u7684Ks\u5206\u5e03\u3002\n\nnewick_tree = (Zijuj, (Rochi, (Madom, (Pravi, (Prten, ((Prper, Prdul), (Prmon, (Prped, Prtri))))))));\n\n# \u6307\u5b9a\u4e00\u4e2a\u7cfb\u7edf\u53d1\u80b2\u6811\uff0c\u8981\u5305\u542b\u6240\u6709\u591a\u500d\u5316\u5206\u6790\u7684\u7269\u79cd\n\nlatin_names =       Madom     : Malus_domestica,\n                    Pravi     : Prunus_avium,\n                    Prdul     : Prunus_dulcis,\n                    Prped     : Prunus_pedunculata,\n                    Prper     : Prunus_persica,\n                    Rochi     : Rosa_chinensis,\n                    Zijuj     : Ziziphus_jujuba,\n                    Prten     : Prunus_tenella,\n                    Prtri     : Prunus_trilpba,\n                    Prmon     : Prunus_mongolica\n\n# \u7269\u79cd\u540d\u5b57\u7684\u7b80\u5199\u548c\u62c9\u4e01\u540d\u5168\u79f0\n\nfasta_filenames =   Madom     : sequence_Prunus\/Malus_domestica_Chr_cds.fa,\n                    Pravi     : sequence_Prunus\/Prunus_avium_Chr_cds.fa,\n                    Prdul     : sequence_Prunus\/Prunus_dulcis_Chr_cds.fa,\n                    Prped     : sequence_Prunus\/Prunus_pedunculata_Chr.cds.fasta,\n                    Prper     : sequence_Prunus\/Prunus_persica_Chr_cds.fa,\n                    Rochi     : sequence_Prunus\/Rosa_chinensis_Chr_cds.fa,\n                    Zijuj     : sequence_Prunus\/Ziziphus_jujuba_Chr_cds.fa,\n                    Prten     : sequence_Prunus\/Prunus_tenella_chr.cds.fasta,\n                    Prtri     : sequence_Prunus\/Prunus_trilpba_trimmed.cds,\n                    Prmon     : sequence_Prunus\/Prunus_mongolica_trimmed.cds\n\n# \u6307\u5b9a\u6240\u6709\u7269\u79cd\u7684cds\u6587\u4ef6\u8def\u5f84\n\ngff_filename = \/home\/majunpeng\/sda2\/Biantao_Sequence_data\/Anno\/Final_result\/Prunus_pedunculata_Chr.gff\n# \u6307\u5b9a\u7126\u70b9\u7269\u79cd\u7684\u6ce8\u91ca\u4fe1\u606fgff\u6587\u4ef6\u8def\u5f84\uff0c\u662f\u4e00\u4e2a\u53ef\u9009\u9879\uff0c\u53ef\u4ee5\u4e0d\u63d0\u4f9b\u3002\n\n[ANALYSIS SETTING]\nparanome = yes\ncollinearity = no\nreciprocal_retention = no\ngff_feature = mrna\ngff_attribute = id\nmax_number_outgroups = 4\nconsensus_mode_for_multiple_outgroups = mean among outgroups\n\n[PARAMETERS]\nx_axis_max_limit_paralogs_plot = 5\nbin_width_paralogs = 0.1\ny_axis_max_limit_paralogs_plot = None\nnum_bootstrap_iterations = 200\ndivergence_colors =  Red, MediumBlue, Goldenrod, Crimson, ForestGreen, Gray, SaddleBrown, Black\nx_axis_max_limit_orthologs_plots = 5\nbin_width_orthologs = 0.1\nmax_ks_paralogs = 5\nmax_ks_orthologs = 10\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-0c08798 elementor-widget elementor-widget-code-highlight\" data-id=\"0c08798\" 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>head config_expert.txt\r\n\r\n[EXPERT PARAMETERS]\r\n\r\nlogging_level = info\r\npreserve_ks_tmp_files = no\r\nkde_bandwidth_modifier = 0.4\r\nplot_adjustment_arrows = yes\r\nmax_mixture_model_iterations = 600\r\nnum_mixture_model_initializations = 10\r\nextra_paralogs_analyses_methods = yes\r\nmax_mixture_model_components = 5\r\nmax_mixture_model_ks = 5\r\nmax_gene_family_size = 200\r\ntop_reciprocally_retained_gfs = 2000\r\nuse_original_orthomcl_version = no\r\nmin_ks_anchor_pairs = 0<\/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-91ae5bd elementor-widget elementor-widget-text-editor\" data-id=\"91ae5bd\" 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>\u8fd0\u884cKsrates\u8fdb\u884c\u591a\u500d\u5316\u5206\u6790\uff0c\u5e76\u4e14\u7ed8\u56feKs\u5206\u5e03\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-9dfab60 elementor-widget elementor-widget-code-highlight\" data-id=\"9dfab60\" 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>nextflow run VIB-PSB\/ksrates -profile docker --config config_elaeis.txt --expert config_expert.txt<\/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-75d0f8e elementor-widget elementor-widget-heading\" data-id=\"75d0f8e\" 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\">3.2 \u4f30\u7b97\u591a\u500d\u5316\u65f6\u95f4<\/h3>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-faab250 elementor-widget elementor-widget-text-editor\" data-id=\"faab250\" 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>\u5206\u6790\u539f\u7406\u5176\u5b9e\u5f88\u7b80\u5355\uff0c\u5c31\u662f\u628aWGD\u4ea7\u751f\u7684\u57fa\u56e0\u5bf9\u5206\u6210\u4e24\u7ec4\uff0c\u7136\u540e\u901a\u8fc7Mcmctree\u8fdb\u884c\u5206\u5316\u65f6\u95f4\u7684\u4f30\u7b97\uff0c\u8fdb\u800c\u5f97\u5230WGD\u7684\u65f6\u95f4\u3002\u6240\u4ee5\u6211\u4eec\u8981\u51c6\u5907\u4e00\u4e2a\u7cfb\u7edf\u53d1\u80b2\u6811\u548c\u5316\u77f3\u65f6\u95f4\uff0cmcmctree\u7684\u65f6\u5019\u8981\u7528\u5230\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-2f8fc81 elementor-widget elementor-widget-code-highlight\" data-id=\"2f8fc81\" 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># \u7b5b\u9009\u540c\u6e90\u57fa\u56e0\nwgd dmd Prunus_pedunculata_Chr.cds.fasta -o Prunus_pedunculata_dmd\n# \u8ba1\u7b97KS\nwgd ksd Prunus_pedunculata_dmd\/Prunus_pedunculata_Chr.cds.fasta.tsv ..\/..\/..\/Anno\/Final_result\/Prunus_pedunculata_Chr.cds.fasta -o Prunus_pedunculata_ksd -n 50\n# \u5171\u7ebf\u6027\u5206\u6790\nsyn -f mRNA -a ID Prunus_pedunculata_dmd\/Prunus_pedunculata_Chr.cds.fasta.tsv Prunus_pedunculata_Chr.gff -ks Prunus_pedunculata_ksd\/Prunus_pedunculata_Chr.cds.fasta.tsv.ks.tsv\n# \u62df\u5408\u5cf0\u503cwgd peak --heuristic Prunus_pedunculata_ksd\/Prunus_pedunculata_Chr.cds.fasta.tsv.ks.tsv -ap wgd_syn\/iadhore-out\/anchorpoints.txt -sm wgd_syn\/iadhore-out\/segments.txt -le wgd_syn\/iadhore-out\/list_elements.txt -mp wgd_syn\/iadhore-out\/multiplicon_pairs.txt -o wgd_peak\n# \u7b5b\u9009\u540c\u6e90\u57fa\u56e0\uff0c\u8fd9\u4e00\u6b65\u8981\u52a0\u4e0a\u6240\u6709\u7cfb\u7edf\u53d1\u80b2\u5c5e\u4e0a\u7269\u79cd\u7684cds\u5e8f\u5217\uff0c\u540c\u65f6\u7b5b\u9009\u76f4\u7cfb\u540c\u6e90\u57fa\u56e0\u548c\u65c1\u7cfb\u540c\u6e90\u57fa\n\u56e0\nwgd dmd -f Prunus_pedunculata -ap wgd_peak\/AnchorKs_FindPeak\/Prunus_pedunculata.tsv.ks.tsv_95%CI_AP_for_dating_weighted_format.tsv -o wgd_dmd_ortho Amborella_trichopoda Arabidopsis_thaliana Aristolochia_fimbriata Chloranthus_sessilifolius Dryas_drummondii Helianthus_annuus Malus_domestica Oryza_sativa Papaver_somniferum Prunus_avium Prunus_dulcis Prunus_pedunculata Prunus_persica Rosa_chinensis Spiraea_crenata Vitis_vinifera Ziziphus_jujuba\n# \u4f30\u7b97WGD\u5206\u5316\u65f6\u95f4\nwgd focus --protcocdating --aamodel lg wgd_dmd_ortho\/merge_focus_ap.tsv -sp Reroot.tre -o wgd_dating -d mcmctree -ds 'burnin = 2000' -ds 'sampfreq = 1000' -ds 'nsample = 20000'Spiraea_crenata Amborella_trichopoda Arabidopsis_thaliana Aristolochia_fimbriata Chloranthus_sessilifolius Dryas_drummondii Helianthus_annuus Malus_domestica Oryza_sativa Papaver_somniferum Prunus_avium Prunus_dulcis Prunus_persica Rosa_chinensis Spiraea_crenata Vitis_vinifera Ziziphus_jujuba Prunus_pedunculata<\/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\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 \u63d0\u8d77\u591a\u500d\u5316\uff08WGD\uff09\u5206\u6790\u8f6f\u4ef6\uff0c\u5927\u5bb6\u7b2c\u4e00\u65f6\u95f4\u60f3\u5230\u7684\u90fd\u662fWGDI\uff0c\u4f46\u662f\u5176\u5b9e\u8fd8\u6709\u53e6\u5916\u4e00\u6b3e\u8f6f\u4ef6\u4e5f\u80fd\u505a\u591a\u500d\u5316 &#8230; <a title=\"\u591a\u500d\u5316\u5206\u6790\u8f6f\u4ef6\u7684\u7684\u53e6\u4e00\u4e2a\u9009\u62e9\u201cWGD V2\u201d\" class=\"read-more\" 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