{"id":2463,"date":"2025-12-02T10:44:06","date_gmt":"2025-12-02T02:44:06","guid":{"rendered":"http:\/\/www.majunpeng.com\/?p=2463"},"modified":"2025-12-04T22:28:16","modified_gmt":"2025-12-04T14:28:16","slug":"aphylogeo%ef%bc%8c%e9%80%82%e5%ba%94%e6%80%a7%e6%bc%94%e5%8c%96%e5%ae%8c%e6%95%b4%e5%a5%97%e4%bb%b6","status":"publish","type":"post","link":"http:\/\/www.majunpeng.com\/index.php\/2025\/12\/02\/aphylogeo%ef%bc%8c%e9%80%82%e5%ba%94%e6%80%a7%e6%bc%94%e5%8c%96%e5%ae%8c%e6%95%b4%e5%a5%97%e4%bb%b6\/","title":{"rendered":"aPhyloGeo\uff0c\u9002\u5e94\u6027\u6f14\u5316\u5b8c\u6574\u5957\u4ef6"},"content":{"rendered":"\t\t<div data-elementor-type=\"wp-post\" data-elementor-id=\"2463\" class=\"elementor elementor-2463\" data-elementor-post-type=\"post\">\n\t\t\t\t<div class=\"elementor-element elementor-element-83f06d6 e-flex e-con-boxed e-con e-parent\" data-id=\"83f06d6\" 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-0283d02 elementor-widget elementor-widget-heading\" data-id=\"0283d02\" 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. \u5f15\u8a00<\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-aa24666 elementor-widget elementor-widget-text-editor\" data-id=\"aa24666\" 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>\u7c7b\u7fa4\u7684\u9002\u5e94\u6027\u7814\u7a76\u4e00\u76f4\u662f\u7cfb\u7edf\u53d1\u80b2\u7814\u7a76\u7684\u4e0b\u6e38\uff0c\u540c\u65f6\u4e5f\u662f\u5c06\u4f20\u7edf\u7684\u5206\u7c7b\u5b66\u95ee\u9898\u5347\u534e\u5230\u7269\u79cd\u591a\u6837\u6027\u7684\u91cd\u8981\u6865\u6881\u3002\u4f46\u662f\uff0c\u4f20\u7edf\u7684\u9002\u5e94\u6027\u6f14\u5316\u5927\u90e8\u5206\u90fd\u505c\u7559\u5728\u901a\u8fc7\u4eba\u4e3a\u7684\u5c06\u7cfb\u7edf\u53d1\u80b2\u6811\u6216\u8005\u591a\u6837\u5316\u901f\u7387\u4e0e\u4e00\u4e9b\u6c14\u5019\u56e0\u5b50\u6570\u636e\u6216\u8005\u6d77\u62d4\u76f8\u4e92\u8054\u7cfb\uff0c\u5f88\u96be\u8fdb\u884c\u91cf\u5316\u3002\u4eca\u5929\u6765\u4ecb\u7ecd\u4e00\u4e2a\u65b0\u7684\u8f6f\u4ef6aPhyloGeo\uff0c\u8fd9\u4e2a\u8f6f\u4ef6\u4e3b\u8981\u7684\u7b97\u6cd5\u5c31\u662f\u901a\u8fc7\u5c06\u57fa\u4e8e\u6c14\u5019\u56e0\u5b50\u6784\u5efa\u7684\u805a\u7c7b\u6811\u548c\u57fa\u4e8e\u9057\u4f20\u4fe1\u606f\uff08\u57fa\u56e0\uff09\u6784\u5efa\u7684\u57fa\u56e0\u6811\u7684\u62d3\u6251\u7ed3\u6784\u8fdb\u884c\u6bd4\u8f83\uff0c\u4ece\u800c\u627e\u5230\u548c\u7279\u5b9a\u6c14\u5019\u56e0\u5b50\u76f8\u5173\u8054\u7684\u57fa\u56e0\uff0c\u4e5f\u5c31\u786e\u5b9a\u4e86\u90a3\u4e9b\u57fa\u56e0\u9a71\u52a8\u4e86\u7c7b\u7fa4\u7684\u9002\u5e94\u6027\u6f14\u5316\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-740e1b9 elementor-widget-divider--view-line elementor-widget elementor-widget-divider\" data-id=\"740e1b9\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"divider.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<div class=\"elementor-divider\">\n\t\t\t<span class=\"elementor-divider-separator\">\n\t\t\t\t\t\t<\/span>\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-bc52cc7 elementor-widget elementor-widget-heading\" data-id=\"bc52cc7\" 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-d9432b4 elementor-widget elementor-widget-text-editor\" data-id=\"d9432b4\" 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>\u4e2a\u4eba\u770b\u4e86\u534a\u4e2a\u5c0f\u65f6\u7684\u5b98\u65b9\u4e0b\u8f7d\u6559\u7a0b\uff0c\u5e76\u4e14\u5728Gemini\u7684\u5e2e\u52a9\u4e0b\uff0c\u624d\u641e\u660e\u767d\u8fd9\u4e2a\u8f6f\u4ef6\u7684\u5b89\u88c5\u548c\u4f7f\u7528\u903b\u8f91\uff0c\u771f\u7684\u5f88\u53cd\u4eba\u7c7b\u3002\u903b\u8f91\u5927\u6982\u5c31\u662f\u8981\u901a\u8fc7poetry\u8fd9\u4e2a\u8f6f\u4ef6\uff0c\u8fdb\u5165\u4f5c\u8005\u914d\u7f6e\u5728\u5b89\u88c5\u8def\u5f84\u4e2d\u7684\u4e00\u4e2a\u73af\u5883\uff0c\u5728\u8fd9\u4e2a\u73af\u5883\u5b8c\u6210\u540e\u7eed\u7684\u5206\u6790\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-56f7ade elementor-widget elementor-widget-code-highlight\" data-id=\"56f7ade\" 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>git clone https:\/\/github.com\/tahiri-lab\/aPhyloGeo.git\ncd aPhyloGeo\npip install poetry\npoetry install\npoetry self add poetry-plugin-shell\n# \u8fdb\u5165\u73af\u5883\npoetry shell<\/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-18f1355 elementor-widget-divider--view-line elementor-widget elementor-widget-divider\" data-id=\"18f1355\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"divider.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<div class=\"elementor-divider\">\n\t\t\t<span class=\"elementor-divider-separator\">\n\t\t\t\t\t\t<\/span>\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-fb81c08 elementor-widget elementor-widget-heading\" data-id=\"fb81c08\" 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 \u8f6f\u4ef6\u4f7f\u7528<\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-90869e2 elementor-widget elementor-widget-text-editor\" data-id=\"90869e2\" 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>\u5728\u5f15\u8a00\u91cc\u9762\u8bf4\u4e86\uff0c\u8fd9\u4e2a\u8f6f\u4ef6\u5176\u5b9e\u548c\u6839\u636e\u57fa\u56e0\u6784\u5efa\u7684\u9057\u4f20\u4fe1\u606f\u6811\u548c\u73af\u5883\u56e0\u5b50\u6784\u5efa\u7684\u805a\u7c7b\u6811\u8fdb\u884c\u7ed3\u6784\u76f8\u4f3c\u6027\u6bd4\u8f83\uff0c\u4ece\u800c\u5f97\u51fa\u54ea\u4e2a\u73af\u5883\u56e0\u5b50\u548c\u90a3\u4e9b\u57fa\u56e0\u6216\u8005\u90a3\u4e00\u6bb5\u57fa\u56e0\u5177\u6709\u76f8\u5173\u6027\uff0c\u6240\u4ee5\u7b2c\u4e00\u6b65\u5c31\u662f\u51c6\u5907\u6bcf\u4e2a\u6837\u672c\uff08\u7269\u79cd\uff09\u91c7\u6837\u5730\u70b9\u7684\u73af\u5883\u4fe1\u606f\uff0c\u4f8b\u5982\u5e73\u5747\u6c14\u6e29\uff0c\u964d\u6c34\u91cf\u7b49\u7b49\u3002\u8fd9\u65f6\u5019\u53ef\u80fd\u4f1a\u6709\u51fa\u73b0\u95ee\u9898\u4e86\uff0c\u8c01\u91c7\u6837\u7684\u65f6\u5019\u4f1a\u8bb0\u5f55\u4ec0\u4e48\u6c14\u6e29\uff0c\u964d\u6c34\u91cf\u554a\uff1f\u786e\u5b9e\uff0c\u5982\u679c\u4e0d\u662f\u4e13\u95e8\u505a\u751f\u6001\u6216\u8005\u73af\u5883\u8c03\u67e5\u7684\u4e0d\u4f1a\u8bb0\u5f55\u8fd9\u4e9b\u3002\u4f46\u662f\u6ca1\u5173\u7cfb\uff0c\u6211\u4eec\u6709\u91c7\u6837\u70b9\u548c\u7ecf\u7eac\u5ea6\u554a\uff0c\u53ef\u4ee5\u57fa\u4e8eWorldClim\u768419\u4e2a\u751f\u7269\u56e0\u5b50\u7684\u6570\u636e\uff0c\u5f97\u5230\u6211\u4eec\u6bcf\u4e2a\u6837\u672c\u7684\u91c7\u6837\u70b9\u5bf9\u5e94\u7684\u4e00\u4e9b\u73af\u5883\u56e0\u5b50\u7684\u6570\u636e\uff0c\u8fd9\u6837\u5c31\u89e3\u51b3\u4e86\u6211\u4eec\u5206\u6790\u7684\u95ee\u9898\uff0c\u56e0\u6b64\u7b2c\u4e00\u6b65\u5c31\u662f\u6839\u636e\u91c7\u6837\u70b9\u7684\u7ecf\u7eac\u5ea6\u548c19\u4e2a\u6c14\u5019\u56e0\u5b50\uff0c\u5f97\u5230\u6bcf\u4e2a\u91c7\u6837\u70b9\u7684\u73af\u5883\u56e0\u5b50\u6570\u636e\uff0c\u81f3\u4e8e\u600e\u4e48\u4e0b\u8f7d19\u4e2a\u6c14\u5019\u56e0\u5b50\uff0c\u8bf7\u81ea\u884c\u7f51\u4e0a\u67e5\u627e\u5b66\u4e60\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-25c6783 elementor-widget elementor-widget-heading\" data-id=\"25c6783\" 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\">\u51c6\u5907\u4e00\u4e2acsv\u683c\u5f0f\uff0c\u6837\u54c1\u7684\u7ecf\u7eac\u5ea6\u548c\u6d77\u62d4\u6570\u636e\uff08\u6d77\u62d4\u53ef\u4ee5\u6ca1\u6709\uff0c\u662f\u53ef\u9009\u7684\uff09<\/h3>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-d7eb3ab elementor-widget elementor-widget-shortcode\" data-id=\"d7eb3ab\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"shortcode.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<div class=\"elementor-shortcode\">\n<table id=\"tablepress-25\" class=\"tablepress tablepress-id-25\">\n<thead>\n<tr class=\"row-1 odd\">\n\t<th class=\"column-1\">ID<\/th><th class=\"column-2\">Longitude<\/th><th class=\"column-3\">Latitude<\/th><th class=\"column-4\">Altitude<\/th>\n<\/tr>\n<\/thead>\n<tbody class=\"row-hover\">\n<tr class=\"row-2 even\">\n\t<td class=\"column-1\">Sample_01<\/td><td class=\"column-2\">114.3<\/td><td class=\"column-3\">30.6<\/td><td class=\"column-4\">20<\/td>\n<\/tr>\n<tr class=\"row-3 odd\">\n\t<td class=\"column-1\">Sample_02<\/td><td class=\"column-2\">116.4<\/td><td class=\"column-3\">39.9<\/td><td class=\"column-4\">50<\/td>\n<\/tr>\n<tr class=\"row-4 even\">\n\t<td class=\"column-1\">Sample_03<\/td><td class=\"column-2\">121.47<\/td><td class=\"column-3\">31.23<\/td><td class=\"column-4\">10<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<!-- #tablepress-25 from cache --><\/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-5c57298 elementor-widget elementor-widget-heading\" data-id=\"5c57298\" 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\">\u7ecf\u7eac\u5ea6\u8f6c\u5316\u4e3a\u73af\u5883\u56e0\u5b50\uff0c\u8f93\u51fa\u7684\u6587\u4ef6\u5c31\u662faPhyloGeo\u7684\u5176\u4e2d\u7684\u4e00\u4e2a\u8f93\u5165\u6587\u4ef6<\/h3>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-f8dc6ba elementor-widget elementor-widget-code-highlight\" data-id=\"f8dc6ba\" 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 ~\/Gemini\/Location2enviroment_1.py -c coordinates.csv -t wc_data -o test.csv\n\nhead test.csv\nID,Precipitation_of_Driest_Quarter,Mean_Temperature_of_Warmest_Quarter,Max_Temperature_of_Warmest_Month,Mean_Temperature_of_Wettest_Quarter,Precipitation_of_Wettest_Quarter,Temperature_Annual_Range,Mean_Temperature_of_Coldest_Quarter,Precipitation_of_Driest_Month,Min_Temperature_of_Coldest_Month,Isothermality,Precipitation_Warmest_Quarter,Annual_Mean_Temperature,Precipitation_Seasonality,Precipitation_of_Wettest_Month,Annual_Precipitation,Mean_Diurnal_Range,Temperature_Seasonality,Mean_Temperature_of_Driest_Quarter,Precipitation_of_Coldest_Quarter\nSample_01,129.0,28.108,32.996,25.945333,561.0,32.272,5.813,31.0,0.724,25.054485,510.0,17.257708,54.785477,203.0,1265.0,8.085583,904.89557,7.8065,129.0\nSample_02,14.0,25.4365,31.328,25.4365,440.0,40.255997,-1.7836666,4.0,-8.9279995,28.161226,440.0,12.493875,136.02074,206.0,578.0,11.336583,1107.1929,-1.7836666,14.0\nSample_03,144.0,26.649,31.302,26.614,442.0,29.947,5.8485003,48.0,1.355,23.248016,409.0,16.459126,48.190933,162.0,1061.0,6.9620833,853.7569,13.0485,153.0<\/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-b6fefe5 elementor-widget elementor-widget-text-editor\" data-id=\"b6fefe5\" 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>\u63a5\u4e0b\u6765\u5c31\u662f\u8fd0\u884caPhyloGeo\uff0c\u6211\u4eec\u5df2\u7ecf\u6709\u4e86\u5176\u4e2d\u4e00\u4e2a\u8f93\u5165\u6570\u636e\uff0c\u53e6\u5916\u4e00\u4e2a\u5c31\u662fMAS\u3002\u8fd9\u91cc\u9700\u8981\u6ce8\u610f\u7684\u662f\uff0c\u8fd9\u4e2a\u8f6f\u4ef6\u7684\u8f93\u5165\u6587\u4ef6\u548c\u8f93\u51fa\u6587\u4ef6\u4ee5\u53ca\u4e00\u4e9b\u53c2\u6570\u662f\u901a\u8fc7\u914d\u7f6e\u6587\u4ef6\u8bbe\u7f6e\u7684\uff0c\u5e76\u4e14\u8fd0\u884c\u4e5f\u6bd4\u8f83\u5947\u602a\uff0c\u4e0d\u9700\u8981\u6307\u5b9a\u914d\u7f6e\u6587\u4ef6\u7684\u4f4d\u7f6e\uff0c\u8f6f\u4ef6\u4f1a\u81ea\u5df1\u5bfb\u627e\uff0c\u6240\u4ee5\u914d\u7f6e\u6587\u4ef6\u7684\u4f4d\u7f6e\u662f\u4e0d\u80fd\u6539\u7684\uff0c\u914d\u7f6e\u6587\u4ef6\u7684\u4f4d\u7f6e\u9ed8\u8ba4\u5c31\u5728\u8f6f\u4ef6\u4e0b\u8f7d\u76ee\u5f55\u7684\/aphylogeo\/params.yaml<\/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-e3a5d62 elementor-widget elementor-widget-code-highlight\" data-id=\"e3a5d62\" 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>file_name: '.\/datasets\/example\/geo.csv' # \u4fee\u6539\u4e3a\u521a\u751f\u6210\u7684\u73af\u5883\u56e0\u5b50\u6587\u4ef6\n\nspecimen: 'id' #\"Please enter the name of the column containing the specimens names: \"\ndist_threshold: 60\nwindow_size: 200\nstep_size: 100\nbootstrap_threshold: 100 #The number of bootstrap samples to generate.\nreference_gene_dir: '.\/datasets' # MSA\u6587\u4ef6\u8def\u5f84\nreference_gene_file: 'sequences.fasta' # MSA\u6587\u4ef6\u540d\n\nmakeDebugFiles: True\nalignment_method: '1' #Please select one ~ 0:no alignment, 1:pairwiseAligner, 2:MUSCLE, 3:CLUSTALW, 4:MAFFT\ndistance_method: '0' #Please select one  ~ 0: All distance methods, 1: Least-Square distance, 2: Robinson-Foulds distance, 3: Euclidean distance (DendroPY)\nfit_method: '1' #Please select one ~ 1:Wider Fit by elongating with Gap (starAlignment), 2:Narrow-fit prevent elongation with gap when possible\ntree_type: '1' #Please select one ~ 1: BioPython consensus tree, 2: FastTree application\nrate_similarity: 90\nmethod_similarity: '1' #Please select one :\n    # 1: Hamming distance\n    # 2: Levenshtein distance\n    # 3: Damerau-Levenshtein distance\n    # 4: Jaro similarity\n    # 5: Jaro-Winkler similarity\n    # 6: Smith\u2013Waterman similarity\n    # 7: Jaccard similarity\n    # 8: S\u00f8rensen-Dice similarity\npreprocessing_genetic: 1\npreprocessing_climatic: 1\npreprocessing_threshold_genetic: 0.2   # proportion of gaps allowed\npreprocessing_threshold_climatic: 0.7  #variance threshold for numeric columns\npermutations_mantel_test: 999 #permutations for Mantel test\npermutations_protest: 999 #permutations for PROTEST analysis\nmantel_test_method: \"pearson\" #method for Mantel test\nstatistical_test: '1' #Please select one ~ 0: Both test, 1: Mantel test, 2: PROTEST (Procrustes) analysis<\/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-fa8882a elementor-widget elementor-widget-heading\" data-id=\"fa8882a\" 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\">\u8fd0\u884c<\/h3>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-6ffc7c0 elementor-widget elementor-widget-code-highlight\" data-id=\"6ffc7c0\" 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>make\n\n# head \/result\/output.csv\nGene,Phylogeographic tree,Name of species,Position in ASM,Bootstrap mean,Least-Square Distance,Robinson-Foulds Distance,Normalised RF Dist,Euclidean Distance,window,r (Correlation coeffici>.\/datasets\/example\/sequences.fasta,ALLSKY_SFC_SW_DWN,OL989074,200_399,100.0,3.41,4.0,1.0,0.71,,,,\n.\/datasets\/example\/sequences.fasta,T2M,OL989074,200_399,100.0,3.89,4.0,1.0,0.62,,,,\n.\/datasets\/example\/sequences.fasta,QV2M,OL989074,200_399,100.0,4.54,4.0,1.0,0.67,,,,\n.\/datasets\/example\/sequences.fasta,WS10M,OL989074,200_399,100.0,4.1,4.0,1.0,0.53,,,,\n.\/datasets\/example\/sequences.fasta,ALLSKY_SFC_SW_DWN,OL989074,400_599,100.0,3.4,4.0,1.0,0.71,,,,\n.\/datasets\/example\/sequences.fasta,T2M,OL989074,400_599,100.0,3.88,4.0,1.0,0.62,,,,\n.\/datasets\/example\/sequences.fasta,QV2M,OL989074,400_599,100.0,4.53,2.0,0.5,0.67,,,,\n.\/datasets\/example\/sequences.fasta,WS10M,OL989074,400_599,100.0,4.08,4.0,1.0,0.53,,,,\n.\/datasets\/example\/sequences.fasta,ALLSKY_SFC_SW_DWN,OL989074,600_799,100.0,3.3,4.0,1.0,0.71,,,,\n.\/datasets\/example\/sequences.fasta,T2M,OL989074,600_799,100.0,3.72,4.0,1.0,0.62,,,,\n.\/datasets\/example\/sequences.fasta,QV2M,OL989074,600_799,100.0,4.35,4.0,1.0,0.65,,,,\n.\/datasets\/example\/sequences.fasta,WS10M,OL989074,600_799,100.0,3.91,4.0,1.0,0.52,,,,\n.\/datasets\/example\/sequences.fasta,ALLSKY_SFC_SW_DWN,OL989074,800_999,100.0,3.4,4.0,1.0,0.71,,,,\n.\/datasets\/example\/sequences.fasta,T2M,OL989074,800_999,100.0,3.88,4.0,1.0,0.62,,,,\n.\/datasets\/example\/sequences.fasta,QV2M,OL989074,800_999,100.0,4.53,4.0,1.0,0.67,,,,\n.\/datasets\/example\/sequences.fasta,WS10M,OL989074,800_999,100.0,4.08,4.0,1.0,0.53,,,,\n.\/datasets\/example\/sequences.fasta,ALLSKY_SFC_SW_DWN,OL989074,1000_1199,100.0,3.41,4.0,1.0,0.71,,,,\n.\/datasets\/example\/sequences.fasta,T2M,OL989074,1000_1199,100.0,3.89,4.0,1.0,0.62,,,,\n.\/datasets\/example\/sequences.fasta,QV2M,OL989074,1000_1199,100.0,4.54,4.0,1.0,0.67,,,,\n.\/datasets\/example\/sequences.fasta,WS10M,OL989074,1000_1199,100.0,4.1,4.0,1.0,0.53,,,,\n,,,,,,,,,Mantel test result:,-0.4671097202423033,0.27,5.0<\/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-32f9b44 elementor-widget elementor-widget-text-editor\" data-id=\"32f9b44\" 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>\u968f\u540e\u4f1a\u5728\u5f53\u524d\u6587\u4ef6\u5939\u4e0b\u751f\u6210\u4e00\u4e2aresult\u6587\u4ef6\u5939\uff0c\u91cc\u9762\u5c31\u662f\u5206\u6790\u7684\u63a5\u8fc7\uff0c\u4e3b\u8981\u770boutput.csv\u5c31\u53ef\u4ee5\u3002\u4e2a\u4eba\u8ba4\u4e3a\u6bd4\u8f83\u91cd\u8981\u7684\u5c31\u662f<strong>Normalised RF Dist\uff08\u8861\u91cf\u57fa\u56e0\u6811\u548c\u73af\u5883\u56e0\u5b50\u6811\u7684\u62d3\u6251\u7ed3\u6784\u76f8\u4f3c\u6027\u6307\u6807\uff09\u3001Mantel test result\uff08\u8861\u91cf\u73af\u5883\u5bf9\u8be5\u7c7b\u7fa4\u5206\u5316\u7684\u4e00\u4e2a\u4f5c\u7528\uff09\u3002<\/strong><\/p><p>| Gene | \u8f93\u5165\u7684\u5e8f\u5217\u6587\u4ef6\u8def\u5f84\uff08.\/datasets\/example\/sequences.fasta\uff09 |<br \/>| Phylogeographic tree | \u73af\u5883\/\u6c14\u5019\u53d8\u91cf\u540d\u79f0\uff0c\u7528\u4e8e\u6784\u5efa\u5730\u7406\u6811 |<br \/>| Name of species | \u7269\u79cd\/\u5e8f\u5217\u6807\u8bc6\u7b26\uff08\u5982 OL989074\uff0c\u8fd9\u662f GenBank \u767b\u5f55\u53f7\uff09 |<br \/>| Position in ASM | \u5e8f\u5217\u6ed1\u52a8\u7a97\u53e3\u4f4d\u7f6e\uff0c\u683c\u5f0f\u4e3a \u8d77\u59cb_\u7ec8\u6b62\uff08\u5982 200_399 \u8868\u793a\u7b2c200-399bp\uff09 |<br \/>| Bootstrap mean | Bootstrap \u5e73\u5747\u503c\uff0c\u8861\u91cf\u7cfb\u7edf\u53d1\u80b2\u6811\u5206\u652f\u7684\u7f6e\u4fe1\u5ea6\uff08100.0 \u8868\u793a\u5b8c\u5168\u652f\u6301\uff09 |<br \/>| Least-Square Distance | \u6700\u5c0f\u4e8c\u4e58\u8ddd\u79bb\uff0c\u8861\u91cf\u7cfb\u7edf\u53d1\u80b2\u6811\u4e0e\u5730\u7406\u6811\u4e4b\u95f4\u7684\u5dee\u5f02 |<br \/>| Robinson-Foulds Distance | Robinson-Foulds \u8ddd\u79bb\uff0c\u6bd4\u8f83\u4e24\u68f5\u6811\u62d3\u6251\u7ed3\u6784\u5dee\u5f02\u7684\u7ecf\u5178\u6307\u6807 |<br \/>| Normalised RF Dist | \u6807\u51c6\u5316 RF \u8ddd\u79bb\uff080-1\u4e4b\u95f4\uff0c1.0 \u8868\u793a\u6811\u7ed3\u6784\u5b8c\u5168\u4e0d\u540c\uff09 |<br \/>| Euclidean Distance | \u6b27\u6c0f\u8ddd\u79bb\uff0c\u8861\u91cf\u4e24\u68f5\u6811\u4e4b\u95f4\u7684\u8ddd\u79bb |<br \/>| window | \u7a97\u53e3\u4fe1\u606f\uff08\u6b64\u5904\u4e3a\u7a7a\uff09 |<br \/>| r (Correlation coefficient) | Mantel \u68c0\u9a8c\u76f8\u5173\u7cfb\u6570\uff08\u4ec5\u6700\u540e\u4e00\u884c\u6709\u503c\uff1a-0.467\uff09 |<br \/>| p (Significance level) | Mantel \u68c0\u9a8c\u663e\u8457\u6027\u6c34\u5e73\uff080.27\uff0c&gt;0.05 \u8868\u793a\u4e0d\u663e\u8457\uff09 |<br \/>| n (Number of observations) | \u89c2\u6d4b\u6570\u91cf\uff085\u4e2a\u6837\u672c\uff09<\/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-74dc6ab elementor-widget-divider--view-line elementor-widget elementor-widget-divider\" data-id=\"74dc6ab\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"divider.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<div class=\"elementor-divider\">\n\t\t\t<span class=\"elementor-divider-separator\">\n\t\t\t\t\t\t<\/span>\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-75826e0 elementor-widget elementor-widget-heading\" data-id=\"75826e0\" 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. \u7ed3\u8bed\n<\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-6ba9879 elementor-widget elementor-widget-text-editor\" data-id=\"6ba9879\" 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>\u7531\u4e8e\u4e00\u4e9b\u4e0d\u53ef\u6297\u529b\u7684\u539f\u56e0\uff0c\u8fd9\u4e2a\u535a\u5ba2\u5199\u4e86\u4e09\u5929\u624d\u5199\u5b8c\u3002\u6211\u89c9\u5f97\u8fd9\u4e2a\u8f6f\u4ef6\u5728\u751f\u7269\u591a\u6837\u6027\u7814\u7a76\u9886\u57df\u662f\u6709\u5f88\u9ad8\u6f5c\u529b\u7684\uff0c\u6bd4\u5982\u7814\u7a76\u67d0\u4e2a\u5730\u7406\u90e8\u5206\u5f88\u6709\u7279\u70b9\u7684\u7c7b\u7fa4\uff0c\u5c31\u53ef\u4ee5\u77e5\u9053\u90a3\u4e9b\u73af\u5883\u56e0\u7d20\u662f\u771f\u6b63\u63a8\u52a8\u4e86\u7269\u79cd\u7684\u591a\u6837\u5316\uff0c\u800c\u4e0d\u662f\u5728\u8ba8\u8bba\u91cc\u9762\u610f\u6deb\u3002\u53e6\u5916\uff0c\u8f6f\u4ef6\u7684\u672c\u8eab\u5176\u5b9e\u6709\u4e00\u4e9b\u5c40\u9650\u6027\uff0c\u5728\u5206\u6790\u7684\u8fc7\u7a0b\u4e2d\uff0c\u662f\u5229\u7528\u5355\u4e2a\u57fa\u56e0\u91c7\u7528\u6ed1\u52a8\u7a97\u53e3\u7684\u5f62\u5f0f\u8fdb\u884c\u6784\u5efa\u591a\u4e2a\u7cfb\u7edf\u53d1\u80b2\uff0c\u4ece\u800c\u8861\u91cf\u6bcf\u4e2a\u7a97\u53e3\u7684\u7684\u57fa\u56e0\u6811\u548c\u73af\u5883\u56e0\u5b50\u6811\u7684\u62d3\u6251\u7ed3\u6784\u76f8\u4f3c\u6027\uff0c\u4ece\u800c\u8fdb\u884c\u5224\u65ad\u76f8\u5173\u6027\u3002\u4f46\u662f\u5728\u5927\u591a\u6570\u7684\u60c5\u51b5\u4e0b\uff0c\u90fd\u662f\u591a\u57fa\u56e0\u5efa\u6811\uff0c\u5c11\u5219\u51e0\u5341\uff0c\u591a\u5219\u51e0\u767e\u4e0a\u5343\uff0c\u548c\u8f6f\u4ef6\u4f5c\u8005\u7684\u7684\u8bbe\u60f3\u8fd8\u662f\u4e0d\u592a\u4e00\u6837\u3002\u4e2a\u4eba\u8ba4\u4e3a\u5982\u679c\u5728\u771f\u5b9e\u7684\u7814\u7a76\u4e2d\uff0c\u6709\u4e24\u79cd\u7b56\u7565\uff081\uff09\u6211\u4eec\u53ef\u4ee5\u628a\u591a\u4e2a\u57fa\u56e0\u4e32\u8054\u8d77\u6765\uff0c\u7136\u540e\u6ed1\u52a8\u7a97\u53e3\uff0c\u6700\u540e\u7b5b\u9009\u51fa\u548c\u73af\u5883\u56e0\u5b50\u5177\u6709\u76f8\u5173\u6027\u7684\u7247\u6bb5\uff0c\u5e76\u8fdb\u4e00\u6b65\u627e\u51fa\u8fd9\u4e9b\u7247\u6bb5\u6765\u81ea\u4e8e\u90a3\u4e9b\u57fa\u56e0\uff1b\uff082\uff09\u6bcf\u4e2a\u57fa\u56e0\u5355\u72ec\u8fdb\u884c\u4e00\u6b21\u5206\u6790\uff0c\u6700\u540e\u5bf9\u7ed3\u679c\u8fdb\u884c\u6c47\u603b\u3002<\/p>\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. 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