{"id":2252,"date":"2025-10-18T18:41:28","date_gmt":"2025-10-18T10:41:28","guid":{"rendered":"http:\/\/www.majunpeng.com\/?p=2252"},"modified":"2025-10-18T19:36:34","modified_gmt":"2025-10-18T11:36:34","slug":"%e5%9f%ba%e4%ba%8ephyloaln%e8%bf%9b%e8%a1%8c%e7%9b%b4%e7%b3%bb%e5%90%8c%e6%ba%90%e5%9f%ba%e5%9b%a0%e7%9a%84%e7%ad%9b%e9%80%89","status":"publish","type":"post","link":"http:\/\/www.majunpeng.com\/index.php\/2025\/10\/18\/%e5%9f%ba%e4%ba%8ephyloaln%e8%bf%9b%e8%a1%8c%e7%9b%b4%e7%b3%bb%e5%90%8c%e6%ba%90%e5%9f%ba%e5%9b%a0%e7%9a%84%e7%ad%9b%e9%80%89\/","title":{"rendered":"\u57fa\u4e8ePhyloAln\u8fdb\u884c\u76f4\u7cfb\u540c\u6e90\u57fa\u56e0\u7684\u7b5b\u9009"},"content":{"rendered":"\t\t<div data-elementor-type=\"wp-post\" data-elementor-id=\"2252\" class=\"elementor elementor-2252\" data-elementor-post-type=\"post\">\n\t\t\t\t<div class=\"elementor-element elementor-element-dfdf474 e-flex e-con-boxed e-con e-parent\" data-id=\"dfdf474\" 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-3bd89df elementor-widget elementor-widget-heading\" data-id=\"3bd89df\" 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-d1cb616 elementor-widget elementor-widget-text-editor\" data-id=\"d1cb616\" 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>\u4e4b\u524d\u5199\u8fc7Hybpiper\u8f6f\u4ef6\u600e\u4e48\u7b5b\u9009\u76f4\u7cfb\u540c\u6e90\u57fa\u56e0\uff0cPhyloAln\u7684\u5de5\u4f5c\u539f\u7406\u548c\u5b83\u5176\u5b9e\u7c7b\u4f3c\uff0c\u4f46\u662f\u5176\u7279\u70b9\u5728\u4e8e\u53ef\u4ee5\u6839\u636e\u4e00\u4e2a\u6bd4\u5bf9\u597d\u7684\u5e8f\u5217\u6587\u4ef6\uff08MSA\uff09\uff0c\u7136\u540e\u4ece\u5176\u4ed6\u6d4b\u5e8f\u6587\u4ef6\u6216<strong>\u5e8f\u5217\u6587\u4ef6<\/strong>\u7b5b\u9009\u76f4\u7cfb\u540c\u6e90\u57fa\u56e0\uff0c\u76f8\u5bf9Hybpiper\uff0c\u591a\u4e86\u4e00\u4e2a\u76f4\u63a5\u4ece\u5e8f\u5217\u7b5b\u9009\u76f4\u7cfb\u540c\u6e90\u57fa\u56e0\u7684\u529f\u80fd\u3002\u7136\u800c\uff0c\u8fd9\u4e2a\u529f\u80fd\u5e76\u4e0d\u662fPhyloAln\u7684\u72ec\u521b\uff0cHamstr\u53ef\u4ee5\u5b8c\u6210\u8fd9\u4e2a\u5de5\u4f5c\uff0c\u4f46\u662f\u8fd9\u4e2a\u8f6f\u4ef6\u7684\u914d\u7f6e\u548c\u8fd0\u884c\u771f\u7684\u592a\u590d\u6742\u4e86\uff0c\u5e76\u4e14\u901f\u5ea6\u5f88\u6162\u3002\u56e0\u6b64\uff0c\u4eca\u5929\u6765\u5b66\u4e60\u4e00\u4e0bPhyloAln\u600e\u4e48\u4f7f\u7528\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-fe49aa0 elementor-widget elementor-widget-heading\" data-id=\"fe49aa0\" 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-efc3df4 elementor-widget elementor-widget-code-highlight\" data-id=\"efc3df4\" 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 phyloaln\nmamba install bioconda::phyloaln<\/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-160dda6 elementor-widget elementor-widget-heading\" data-id=\"160dda6\" 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-c8014dc elementor-widget elementor-widget-text-editor\" data-id=\"c8014dc\" 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<div class=\"ace-line\" dir=\"auto\" data-node=\"true\"><span style=\"color: #ff0000;\"><strong>\u4ee5\u4e0b\u4e3aAI\u603b\u7ed3\uff1a<\/strong><\/span><br \/><span data-leaf=\"true\"><span class=\"lb\">PhyloAln \u7684\u8fd0\u884c\u6d41\u7a0b\u6309\u987a\u5e8f\u5206\u4e3a 5 \u4e2a\u5173\u952e\u6b65\u9aa4\uff0c\u5404\u6b65\u9aa4\u8854\u63a5\u7d27\u5bc6\u4e14\u652f\u6301\u53ef\u9009\u53c2\u6570\u8c03\u6574\uff0c\u5177\u4f53\u5982\u4e0b\uff1a<\/span><\/span><span data-string=\"true\" data-enter=\"true\" data-leaf=\"true\">\u200b<\/span><\/div><div class=\"ace-line heading-h4\" dir=\"auto\" data-node=\"true\"><span data-leaf=\"true\"><span class=\"lb\">1. \u8f93\u5165\u51c6\u5907\u4e0e\u9884\u5904\u7406<\/span><\/span><span data-string=\"true\" data-enter=\"true\" data-leaf=\"true\">\u200b<\/span><\/div><div class=\"ace-line list-div\" dir=\"auto\" data-node=\"true\"><ul class=\"list-bullet1 r-list r-list-bullet\"><li><span data-leaf=\"true\"><span class=\"lb\">\u8f93\u5165\u6587\u4ef6<\/span><\/span><span data-leaf=\"true\"><span class=\"lb\">\uff1a\u9700\u540c\u65f6\u63d0\u4f9b\u4e24\u7c7b\u6838\u5fc3\u6587\u4ef6<\/span><\/span><span data-string=\"true\" data-enter=\"true\" data-leaf=\"true\">\u200b<\/span><\/li><\/ul><\/div><div class=\"ace-line list-div\" dir=\"auto\" data-node=\"true\"><ul class=\"list-bullet2 r-list r-list-bullet\"><li><span data-leaf=\"true\"><span class=\"lb\">\u53c2\u8003\u6587\u4ef6\uff1aFASTA \u683c\u5f0f\u7684\u5df2\u6709\u591a\u5e8f\u5217\u6bd4\u5bf9\u7ed3\u679c\uff08MSA\uff09\uff0c\u53ef\u6765\u81ea\u76f4\u7cfb\u540c\u6e90\u6570\u636e\u5e93\uff08\u5982 OrthoDB\uff09\u6216\u624b\u52a8\u6784\u5efa\uff1b<\/span><\/span><span data-string=\"true\" data-enter=\"true\" data-leaf=\"true\">\u200b<\/span><\/li><\/ul><\/div><div class=\"ace-line list-div\" dir=\"auto\" data-node=\"true\"><ul class=\"list-bullet2 r-list r-list-bullet\"><li><span data-leaf=\"true\"><span class=\"lb\">\u76ee\u6807\u6587\u4ef6\uff1aFASTQ\/FASTA \u683c\u5f0f\u7684\u6d4b\u5e8f reads \u6216\u7ec4\u88c5\u540e\u5e8f\u5217\uff08\u5982\u57fa\u56e0\u7ec4\u7247\u6bb5\u3001\u8f6c\u5f55\u672c\u3001\u86cb\u767d\u8d28\u5e8f\u5217\uff09\u3002<\/span><\/span><span data-string=\"true\" data-enter=\"true\" data-leaf=\"true\">\u200b<\/span><\/li><\/ul><\/div><div class=\"ace-line list-div\" dir=\"auto\" data-node=\"true\"><ul class=\"list-bullet1 r-list r-list-bullet\"><li><span data-leaf=\"true\"><span class=\"lb\">\u9884\u5904\u7406\u64cd\u4f5c<\/span><\/span><span data-leaf=\"true\"><span class=\"lb\">\uff1a<\/span><\/span><span data-string=\"true\" data-enter=\"true\" data-leaf=\"true\">\u200b<\/span><\/li><\/ul><\/div><div class=\"ace-line list-div\" dir=\"auto\" data-node=\"true\"><ul class=\"list-bullet2 r-list r-list-bullet\"><li><span data-leaf=\"true\"><span class=\"lb\">\u6309\u7528\u6237\u9009\u62e9\u7684\u6a21\u5f0f\u5904\u7406\u76ee\u6807\u5e8f\u5217\uff0c\u5982 <\/span><\/span><span data-leaf=\"true\"><span class=\"inline-code inline-code_start inline-code_end\" spellcheck=\"false\"><span class=\"lb\">prot<\/span><\/span><\/span><span data-leaf=\"true\"><span class=\"lb\">\/<\/span><\/span><span data-leaf=\"true\"><span class=\"inline-code inline-code_start inline-code_end\" spellcheck=\"false\"><span class=\"lb\">codon<\/span><\/span><\/span><span data-leaf=\"true\"><span class=\"lb\"> \u6a21\u5f0f\u4e0b\u5c06\u6838\u82f7\u9178\u5e8f\u5217\u7ffb\u8bd1\u6210 6 \u79cd\u9605\u8bfb\u6846\u7684\u86cb\u767d\u8d28\uff0c<\/span><\/span><span data-leaf=\"true\"><span class=\"inline-code inline-code_start inline-code_end\" spellcheck=\"false\"><span class=\"lb\">dna_codon<\/span><\/span><\/span><span data-leaf=\"true\"><span class=\"lb\"> \u6a21\u5f0f\u4e0b\u5904\u7406\u957f\u8bfb\u957f\u7684\u63d2\u5165\u7f3a\u5931\u95ee\u9898\uff1b<\/span><\/span><span data-string=\"true\" data-enter=\"true\" data-leaf=\"true\">\u200b<\/span><\/li><\/ul><\/div><div class=\"ace-line list-div\" dir=\"auto\" data-node=\"true\"><ul class=\"list-bullet2 r-list r-list-bullet\"><li><span data-leaf=\"true\"><span class=\"lb\">\u53ef\u9009\u5bf9\u53c2\u8003 MSA \u6216\u76ee\u6807\u5e8f\u5217\u8fdb\u884c\u7247\u6bb5\u5316\uff08\u5982\u5c06\u957f\u57fa\u56e0\u7ec4\u5e8f\u5217\u62c6\u5206\u4e3a 200bp \u7247\u6bb5\uff0c\u6b65\u957f 100bp\uff09\uff0c\u51cf\u5c11\u5185\u542b\u5b50\u5e72\u6270\u6216\u964d\u4f4e HMM \u641c\u7d22\u8017\u65f6\u3002<\/span><\/span><span data-string=\"true\" data-enter=\"true\" data-leaf=\"true\">\u200b<\/span><\/li><\/ul><\/div><div class=\"ace-line heading-h4\" dir=\"auto\" data-node=\"true\"><span data-leaf=\"true\"><span class=\"lb\">2. HMM \u641c\u7d22\u4e0e\u5e8f\u5217\u6620\u5c04<\/span><\/span><span data-string=\"true\" data-enter=\"true\" data-leaf=\"true\">\u200b<\/span><\/div><div class=\"ace-line\" dir=\"auto\" data-node=\"true\"><span data-leaf=\"true\"><span class=\"lb\">\u8fd9\u662f\u5de5\u5177\u7684\u6838\u5fc3\u6b65\u9aa4\uff0c\u5206\u4e3a \u201c\u641c\u7d22\u5339\u914d\u201d \u548c \u201c\u5750\u6807\u6620\u5c04\u201d \u4e24\u6b65\uff1a<\/span><\/span><span data-string=\"true\" data-enter=\"true\" data-leaf=\"true\">\u200b<\/span><\/div><div class=\"ace-line ol-idPbUf35FI list-div list-start-number1\" dir=\"auto\" data-node=\"true\"><ol class=\"list-number1 r-list r-list-number\" start=\"1\" data-origin-start=\"1\" data-start=\"1\"><li data-start=\"1\"><span data-leaf=\"true\"><span class=\"lb\">HMM \u641c\u7d22\u540c\u6e90\u533a\u57df<\/span><\/span><span data-string=\"true\" data-enter=\"true\" data-leaf=\"true\">\u200b<\/span><\/li><\/ol><\/div><div class=\"ace-line\" dir=\"auto\" data-node=\"true\"><span data-leaf=\"true\"><span class=\"lb\">\u7528 HMMER3 \u5bf9\u9884\u5904\u7406\u540e\u7684\u76ee\u6807\u5e8f\u5217 \/reads \u8fdb\u884c\u641c\u7d22\uff0c\u7b5b\u9009\u51fa\u4e0e\u53c2\u8003 MSA \u540c\u6e90\u7684\u7247\u6bb5\uff0c\u4fdd\u7559\u542b\u4fdd\u5b88\u4f4d\u70b9\u7684\u5339\u914d\u533a\u57df\uff08\u6392\u9664\u968f\u673a\u76f8\u4f3c\u5e8f\u5217\uff09\u3002<\/span><\/span><span data-string=\"true\" data-enter=\"true\" data-leaf=\"true\">\u200b<\/span><\/div><div class=\"ace-line ol-ideXCMZJQ8 list-div\" dir=\"auto\" data-node=\"true\"><ol class=\"list-number1 r-list r-list-number\" start=\"2\" data-origin-start=\"2\" data-start=\"2\"><li data-start=\"2\"><span data-leaf=\"true\"><span class=\"lb\">\u6309\u53c2\u8003\u5750\u6807\u5b9a\u4f4d<\/span><\/span><span data-string=\"true\" data-enter=\"true\" data-leaf=\"true\">\u200b<\/span><\/li><\/ol><\/div><div class=\"ace-line\" dir=\"auto\" data-node=\"true\"><span data-leaf=\"true\"><span class=\"lb\">\u6839\u636e HMMER3 \u8f93\u51fa\u7684\u5339\u914d\u4fe1\u606f\uff0c\u5c06\u76ee\u6807\u5e8f\u5217\u7684\u540c\u6e90\u7247\u6bb5\u6620\u5c04\u5230\u53c2\u8003 MSA \u7684\u5bf9\u5e94\u5750\u6807\u4e0a\uff0c\u540c\u65f6\u4fdd\u7559\u53c2\u8003\u5e8f\u5217\u7684\u95f4\u9699\uff08gap\uff09\u7ed3\u6784\uff0c\u786e\u4fdd\u65b0\u751f\u6210\u7684 MSA \u4e0e\u53c2\u8003\u683c\u5f0f\u4e00\u81f4\uff0c\u65e0\u9700\u91cd\u65b0\u8fdb\u884c\u5168\u5e8f\u5217\u6bd4\u5bf9\u3002<\/span><\/span><span data-string=\"true\" data-enter=\"true\" data-leaf=\"true\">\u200b<\/span><\/div><div class=\"ace-line heading-h4\" dir=\"auto\" data-node=\"true\"><span data-leaf=\"true\"><span class=\"lb\">3. \u53ef\u9009\u6b65\u9aa4\uff1a\u5e8f\u5217\u7ec4\u88c5\uff08\u9488\u5bf9\u77ed\u8bfb\u957f\uff09<\/span><\/span><span data-string=\"true\" data-enter=\"true\" data-leaf=\"true\">\u200b<\/span><\/div><div class=\"ace-line\" dir=\"auto\" data-node=\"true\"><span data-leaf=\"true\"><span class=\"lb\">\u82e5\u8f93\u5165\u4e3a\u77ed\u8bfb\u957f\uff08\u5982 Illumina reads\uff09\uff0c\u53ef\u5f00\u542f \u201c\u91cd\u53e0\u533a\u57df\u7ec4\u88c5\u201d \u529f\u80fd\uff1a<\/span><\/span><span data-string=\"true\" data-enter=\"true\" data-leaf=\"true\">\u200b<\/span><\/div><div class=\"ace-line list-div\" dir=\"auto\" data-node=\"true\"><ul class=\"list-bullet1 r-list r-list-bullet\"><li><span data-leaf=\"true\"><span class=\"lb\">\u57fa\u4e8e\u6620\u5c04\u540e\u7684\u53c2\u8003\u5750\u6807\uff0c\u5c06\u6765\u81ea\u540c\u4e00\u76ee\u6807\u533a\u57df\u3001\u5b58\u5728\u91cd\u53e0\u7684\u77ed reads \u7ec4\u88c5\u6210\u8fde\u7eed\u7247\u6bb5\uff08contig\uff09\uff0c\u8bbe\u5b9a\u91cd\u53e0\u957f\u5ea6\u548c\u4e00\u81f4\u6027\u9608\u503c\uff08\u5982\u91cd\u53e0 50bp\u3001\u4e00\u81f4\u6027 \u226590%\uff09\uff0c\u63d0\u5347\u957f\u7247\u6bb5\u7684\u6bd4\u5bf9\u5b8c\u6574\u6027\u3002<\/span><\/span><span data-string=\"true\" data-enter=\"true\" data-leaf=\"true\">\u200b<\/span><\/li><\/ul><\/div><div class=\"ace-line heading-h4\" dir=\"auto\" data-node=\"true\"><span data-leaf=\"true\"><span class=\"lb\">4. \u53bb\u6c61\u67d3\u5904\u7406\uff08\u6838\u5fc3\u4f18\u52bf\u6b65\u9aa4\uff09<\/span><\/span><span data-string=\"true\" data-enter=\"true\" data-leaf=\"true\">\u200b<\/span><\/div><div class=\"ace-line\" dir=\"auto\" data-node=\"true\"><span data-leaf=\"true\"><span class=\"lb\">PhyloAln \u5185\u7f6e\u4e24\u7c7b\u6c61\u67d3\u53bb\u9664\u673a\u5236\uff0c\u89e3\u51b3\u6d4b\u5e8f\u6570\u636e\u4e2d\u5e38\u89c1\u7684\u5916\u6e90\u6c61\u67d3\uff08\u5982\u5bc4\u751f\u866b\u3001\u5171\u751f\u83cc\uff09\u548c\u4ea4\u53c9\u6c61\u67d3\uff08\u540c\u6279\u6b21\u5176\u4ed6\u7269\u79cd\uff09\u95ee\u9898\uff1a<\/span><\/span><span data-string=\"true\" data-enter=\"true\" data-leaf=\"true\">\u200b<\/span><\/div><div class=\"ace-line ol-idWu2nkAtd list-div list-start-number1\" dir=\"auto\" data-node=\"true\"><ol class=\"list-number1 r-list r-list-number\" start=\"1\" data-origin-start=\"1\" data-start=\"1\"><li data-start=\"1\"><span data-leaf=\"true\"><span class=\"lb\">\u5916\u6e90\u6c61\u67d3\u53bb\u9664<\/span><\/span><span data-string=\"true\" data-enter=\"true\" data-leaf=\"true\">\u200b<\/span><\/li><\/ol><\/div><div class=\"ace-line list-div\" dir=\"auto\" data-node=\"true\"><ul class=\"list-bullet2 r-list r-list-bullet\"><li><span data-leaf=\"true\"><span class=\"lb\">\u8ba1\u7b97\u76ee\u6807\u5e8f\u5217\u4e0e\u53c2\u8003 MSA \u4e2d \u201c\u5916\u7c7b\u7fa4\u201d \u7684 \u201c\u4fdd\u5b88\u6027\u5f97\u5206\u201d\uff08\u57fa\u4e8e\u53c2\u8003\u5e8f\u5217\u4e2d\u78b1\u57fa\u7684\u51fa\u73b0\u9891\u7387\u6c42\u548c\uff09\uff1b<\/span><\/span><span data-string=\"true\" data-enter=\"true\" data-leaf=\"true\">\u200b<\/span><\/li><\/ul><\/div><div class=\"ace-line list-div\" dir=\"auto\" data-node=\"true\"><ul class=\"list-bullet2 r-list r-list-bullet\"><li><span data-leaf=\"true\"><span class=\"lb\">\u82e5\u76ee\u6807\u5e8f\u5217\u7684\u4fdd\u5b88\u6027\u5f97\u5206\u4f4e\u4e8e\u5916\u7c7b\u7fa4\u5f97\u5206\u7684 0.9 \u500d\uff08\u9ed8\u8ba4\u6743\u91cd\uff09\uff0c\u5219\u5224\u5b9a\u4e3a\u5916\u6e90\u6c61\u67d3\u5e76\u79fb\u9664\u3002<\/span><\/span><span data-string=\"true\" data-enter=\"true\" data-leaf=\"true\">\u200b<\/span><\/li><\/ul><\/div><div class=\"ace-line ol-idGn8nO2j0 list-div\" dir=\"auto\" data-node=\"true\"><ol class=\"list-number1 r-list r-list-number\" start=\"2\" data-origin-start=\"2\" data-start=\"2\"><li data-start=\"2\"><span data-leaf=\"true\"><span class=\"lb\">\u4ea4\u53c9\u6c61\u67d3\u53bb\u9664<\/span><\/span><span data-string=\"true\" data-enter=\"true\" data-leaf=\"true\">\u200b<\/span><\/li><\/ol><\/div><div class=\"ace-line list-div\" dir=\"auto\" data-node=\"true\"><ul class=\"list-bullet2 r-list r-list-bullet\"><li><span data-leaf=\"true\"><span class=\"lb\">\u5bf9\u540c\u6279\u6b21\u591a\u4e2a\u76ee\u6807\u7269\u79cd\u7684\u5e8f\u5217\uff0c\u6bd4\u8f83\u4e24\u4e24\u4e4b\u95f4\u7684\u91cd\u53e0\u533a\u57df\uff0c\u82e5\u91cd\u53e0\u957f\u5ea6\u548c\u4e00\u81f4\u6027\u8d85\u8fc7\u9608\u503c\uff0c\u8ba1\u7b97\u4e24\u8005\u7684 \u201c\u4f30\u7b97 RPKM\u201d\uff08\u57fa\u4e8e read \u8ba1\u6570\u548c\u5e8f\u5217\u957f\u5ea6\u7684\u4e30\u5ea6\u6307\u6807\uff09\uff1b<\/span><\/span><span data-string=\"true\" data-enter=\"true\" data-leaf=\"true\">\u200b<\/span><\/li><\/ul><\/div><div class=\"ace-line list-div\" dir=\"auto\" data-node=\"true\"><ul class=\"list-bullet2 r-list r-list-bullet\"><li><span data-leaf=\"true\"><span class=\"lb\">\u82e5\u4e30\u5ea6\u5dee\u5f02\u8d85\u8fc7\u8bbe\u5b9a\u9608\u503c\uff08\u5982 10 \u500d\uff09\uff0c\u5219\u4e30\u5ea6\u4f4e\u7684\u5e8f\u5217\u5224\u5b9a\u4e3a\u6765\u81ea\u4e30\u5ea6\u9ad8\u7684\u7269\u79cd\u7684\u4ea4\u53c9\u6c61\u67d3\uff0c\u4e88\u4ee5\u79fb\u9664\u3002<\/span><\/span><span data-string=\"true\" data-enter=\"true\" data-leaf=\"true\">\u200b<\/span><\/li><\/ul><\/div><div class=\"ace-line heading-h4\" dir=\"auto\" data-node=\"true\"><span data-leaf=\"true\"><span class=\"lb\">5. \u7ed3\u679c\u751f\u6210\u4e0e\u8f93\u51fa<\/span><\/span><span data-string=\"true\" data-enter=\"true\" data-leaf=\"true\">\u200b<\/span><\/div><div class=\"ace-line list-div\" dir=\"auto\" data-node=\"true\"><ul class=\"list-bullet1 r-list r-list-bullet\"><li><span data-leaf=\"true\"><span class=\"lb\">\u5171\u8bc6\u5e8f\u5217\u6784\u5efa<\/span><\/span><span data-leaf=\"true\"><span class=\"lb\">\uff1a\u5bf9\u540c\u4e00\u76ee\u6807\u7269\u79cd\u3001\u540c\u4e00\u53c2\u8003\u5750\u6807\u7684\u591a\u4e2a\u5339\u914d\u5e8f\u5217\uff0c\u53ef\u9009\u751f\u6210\u5171\u8bc6\u5e8f\u5217\uff08\u6309\u78b1\u57fa\u51fa\u73b0\u9891\u7387\u786e\u5b9a\u6bcf\u4e2a\u4f4d\u70b9\u7684\u78b1\u57fa\uff09\uff0c\u51cf\u5c11\u5197\u4f59\uff1b<\/span><\/span><span data-string=\"true\" data-enter=\"true\" data-leaf=\"true\">\u200b<\/span><\/li><\/ul><\/div><div class=\"ace-line list-div\" dir=\"auto\" data-node=\"true\"><ul class=\"list-bullet1 r-list r-list-bullet\"><li><span data-leaf=\"true\"><span class=\"lb\">\u8f93\u51fa\u6587\u4ef6<\/span><\/span><span data-leaf=\"true\"><span class=\"lb\">\uff1a\u751f\u6210 FASTA \u683c\u5f0f\u7684\u65b0 MSA \u6587\u4ef6\uff0c\u5305\u542b\u76ee\u6807\u5e8f\u5217\u4e0e\u53c2\u8003\u5e8f\u5217\u7684\u6574\u5408\u6bd4\u5bf9\u7ed3\u679c\uff1b\u82e5\u4e3a <\/span><\/span><span data-leaf=\"true\"><span class=\"inline-code inline-code_start inline-code_end\" spellcheck=\"false\"><span class=\"lb\">prot<\/span><\/span><\/span><span data-leaf=\"true\"><span class=\"lb\">\/<\/span><\/span><span data-leaf=\"true\"><span class=\"inline-code inline-code_start inline-code_end\" spellcheck=\"false\"><span class=\"lb\">codon<\/span><\/span><\/span><span data-leaf=\"true\"><span class=\"lb\">\/<\/span><\/span><span data-leaf=\"true\"><span class=\"inline-code inline-code_start inline-code_end\" spellcheck=\"false\"><span class=\"lb\">dna_codon<\/span><\/span><\/span><span data-leaf=\"true\"><span class=\"lb\"> \u6a21\u5f0f\uff0c\u8fd8\u4f1a\u989d\u5916\u8f93\u51fa\u5bf9\u5e94\u7684\u86cb\u767d\u8d28\u5e8f\u5217 MSA\uff0c\u76f4\u63a5\u7528\u4e8e\u4e0b\u6e38\u7cfb\u7edf\u53d1\u80b2\u6811\u6784\u5efa\uff08\u5982 IQ-TREE\uff09\u3002<\/span><\/span><\/li><\/ul><\/div>\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-7ec879b elementor-widget-divider--view-line elementor-widget elementor-widget-divider\" data-id=\"7ec879b\" 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-53a2e96 elementor-widget elementor-widget-text-editor\" data-id=\"53a2e96\" 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>PhyloAln\u7684\u539f\u7406\u5176\u5b9e\u5f88\u7b80\u5355\uff0c\u9996\u5148\u6839\u636e\u63d0\u4f9b\u7684\u591a\u5e8f\u5217\u6bd4\u5bf9\u6587\u4ef6\u6784\u5efapHMM\u6a21\u578b\uff0c\u7136\u540e\u901a\u8fc7\u5bf9\u8f93\u5165\u7684Reads\u6216\u8005\u5e8f\u5217\u8fdb\u884c\u641c\u7d22\uff0c\u5982\u679c\u662freads\uff0c\u5219\u8fdb\u884c\u7ec4\u88c5\uff0c\u968f\u540e\u8fc7\u6ee4\uff0c\u6700\u540e\u8f93\u51fa\u76f4\u7cfb\u540c\u6e90\u57fa\u56e0\u3002<strong>\u91cd\u8981\u7684\u4e00\u4e2a\u7279\u70b9\uff0cPhyloAln\u5bf9\u53c2\u8003\u7684\u591a\u5e8f\u5217\u6bd4\u5bf9\u548c\u8f93\u5165\u7684\u6587\u4ef6\u7c7b\u578b\u8981\u6c42\u4e0d\u4e25\u683c\uff0c\u53c2\u8003\u5e8f\u5217\u53ef\u4ee5\u6838\u9178\u548c\u6c28\u57fa\u9178\uff0c\u8f93\u5165\u6587\u4ef6\u53ef\u4ee5\u662f\u6d4b\u5e8f\u6587\u4ef6\uff0c\u6838\u9178\u5e8f\u5217\u548c\u6c28\u57fa\u9178\u5e8f\u5217\uff0c\u7701\u53bb\u4e86\u5f88\u591a\u4e2d\u95f4\u8f6c\u6362\u6b65\u9aa4\u3002<\/strong>\u56e0\u6b64\u6211\u4eec\u9700\u8981\u51c6\u786e\u7684\u8f93\u5165\u6587\u4ef6\u6709\u4e24\u4e2a\uff081\uff09\u53c2\u8003\u7684\u591a\u5e8f\u5217\u6bd4\u5bf9\uff082\uff09\u6d4b\u5e8f\u6587\u4ef6\u6216\u5e8f\u5217\u6587\u4ef6\uff0c\u5e8f\u5217\u6587\u4ef6\u4e00\u822c\u5c31\u662f\u8f6c\u5f55\u7ec4\u9884\u6d4b\u7684cds\/pep\u6216\u8005\u5168\u57fa\u56e0\u7ec4\u6ce8\u91ca\u5f97\u5230\u7684cds\/pep<\/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-5df4426 elementor-widget elementor-widget-code-highlight\" data-id=\"5df4426\" 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># \u5355\u4e2aMSA\u7b5b\u9009\u5355\u4e2a\u6837\u672c\u7684\u76f4\u7cfb\u540c\u6e90\u57fa\u56e0\nPhyloAln -a OG0012156_trimmed_mafft.fa -s Amborella_trichopoda -i Test_pep.fasta -o \noutput_directory -e prot2prot\n\n# -a \u6307\u5b9aMSA\u6587\u4ef6\n# -s \u6307\u5b9aMAS\u6587\u4ef6\u4e2d\u7684\u53c2\u8003\u7269\u79cd\n# -i \u8f93\u5165\u6587\u4ef6\n# -o \u7ed3\u679c\u6587\u4ef6\u5939\n# -e \u8fd0\u884c\u6a21\u5f0f\uff0c\u6839\u636e\u53c2\u8003MSA\u548c\u8f93\u5165\u6587\u4ef6\u7684\u7c7b\u578b\uff0c\u6709\u591a\u79cd\u6a21\u5f0f\uff0cdna2reads,prot2reads,codon2reads,fast_dna2reads,fast_prot2reads,fast_codon2reads,dna2trans,prot2trans,codon2trans,dna2genome,prot2genome,codon2genome,rna2rna,prot2prot,codon2codon,gene_dna2dna,gene_rna2rna,gene_codon2codon,gene_codon2dna,gene_prot2prot}, --mode {dna2reads,prot2reads,codon2reads,fast_dna2reads,fast_prot2reads,fast_codon2reads,dna2trans,prot2trans,codon2trans,dna2genome,prot2genome,codon2genome,rna2rna,prot2prot,codon2codon,gene_dna2dna,gene_rna2rna,gene_codon2codon,gene_codon2dna,gene_prot2prot,\u5177\u4f53\u8bf7\u53c2\u8003\u5b98\u7f51\u8bf4\u660e\uff0c\u672c\u6b21\u5206\u6790\u4f7f\u7528\u7684\u6a21\u5f0f\u662f\u53c2\u8003MSA\u548c\u8f93\u5165\u6587\u4ef6\u5747\u4e3a\u6c28\u57fa\u9178\u5e8f\u5217\u3002<\/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-8f7be92 elementor-widget elementor-widget-text-editor\" data-id=\"8f7be92\" 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>\u5982\u679c\u6709\u591a\u4e2aMSA\u6587\u4ef6\uff0c\u53ef\u4ee5\u4f7f\u7528-d\u66ff\u6362-a\uff0c\u6307\u5b9a\u4e00\u4e2a\u5305\u542b\u6240\u6709MSA\u6587\u4ef6\u7684\u76ee\u5f55\u3002\u540c\u6837\uff0c\u5982\u679c\u6709\u591a\u4e2a\u8f93\u5165\u6587\u4ef6\uff0c\u53ef\u4ee5-c\u66ff\u6362-i\uff0c\u6307\u5b9a\u4e00\u4e2a2\u5217\u7684txt\u6587\u4ef6\uff0c\u7b2c\u4e00\u5217\u4e3a\u6837\u672c\u540d\uff0c\u7b2c\u4e8c\u5217\u4e3a\u8f93\u5165\u6587\u4ef6\u7684\u7edd\u5bf9\u8def\u5f84\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-6877954 elementor-widget elementor-widget-code-highlight\" data-id=\"6877954\" 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>Test1   \/home\/majunpeng\/sda2\/Biantao_Sequence_data\/Comparative_genomics\/Use_data\/Longest_gff\/Prunus_avium_Chr.pep\nTest2   \/home\/majunpeng\/sda2\/Biantao_Sequence_data\/Comparative_genomics\/Use_data\/Longest_gff\/Rosa_chinensis_Chr.pep\nTest3   \/home\/majunpeng\/sda2\/Biantao_Sequence_data\/Anno\/Final_result\/Prunus_pedunculata_Chr.pep.fasta<\/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-7d88d35 elementor-widget elementor-widget-code-highlight\" data-id=\"7d88d35\" 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># \u591a\u4e2aMSA\u7b5b\u9009\u591a\u4e2a\u6837\u672c\u7684\u76f4\u7cfb\u540c\u6e90\u57fa\u56e0\nPhyloAln -d ~\/sda2\/Biantao_Sequence_data\/Comparative_genomics\/Phylo\/renamed_fasta\/Single_Copy_Orthologue_Sequences\/Rename_dir\/mafft -s Amborella_trichopoda  -c Sample.txt  -o output_directory -e prot2prot<\/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-366187b elementor-widget elementor-widget-heading\" data-id=\"366187b\" 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\u679c<\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-7c827c7 elementor-widget elementor-widget-text-editor\" data-id=\"7c827c7\" 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>\u7ed3\u679c\u6587\u4ef6\u5939\u4e2d\u7684\u201cnt_out\u201d\u6709\u6700\u540e\u7b5b\u9009\u51fa\u6765\u7684\u76f4\u7cfb\u540c\u6e90\u57fa\u56e0\uff0c\u8f6f\u4ef6\u8fd8\u5f88\u8d34\u5fc3\uff0c\u628a\u65b0\u7b5b\u9009\u51fa\u6765\u7684\u548c\u539f\u672c\u4f5c\u4e3a\u53c2\u8003\u7684\u76f4\u63a5\u5408\u5e76\u5230\u4e00\u8d77\u8f93\u51fa\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-d130a3d elementor-widget elementor-widget-code-highlight\" data-id=\"d130a3d\" 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>>Amborella_trichopoda\n>Arabidopsis_thaliana\n>Aristolochia_fimbriata\n>Chloranthus_sessilifolius\n>Dryas_drummondii\n>Helianthus_annuus\n>Malus_domestica\n>Oryza_sativa\n>Papaver_somniferum\n>Prunus_avium\n>Prunus_dulcis\n>Prunus_pedunculata\n>Prunus_persica\n>Rosa_chinensis\n>Spiraea_crenata\n>Vitis_vinifera\n>Ziziphus_jujuba\n>Test1.OG0012156_trimmed_mafft.1\n>Test2.OG0012156_trimmed_mafft.1\n>Test3.OG0012156_trimmed_mafft.1\n\n# \u540e\u4e09\u4e2a\u5c31\u662f\u65b0\u7b5b\u9009\u51fa\u6765\u7684\u76f4\u7cfb\u540c\u6e90\u57fa\u56e0\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\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 \u4e4b\u524d\u5199\u8fc7Hybpiper\u8f6f\u4ef6\u600e\u4e48\u7b5b\u9009\u76f4\u7cfb\u540c\u6e90\u57fa\u56e0\uff0cPhyloAln\u7684\u5de5\u4f5c\u539f\u7406\u548c\u5b83\u5176\u5b9e\u7c7b\u4f3c\uff0c\u4f46\u662f\u5176\u7279 &#8230; <a title=\"\u57fa\u4e8ePhyloAln\u8fdb\u884c\u76f4\u7cfb\u540c\u6e90\u57fa\u56e0\u7684\u7b5b\u9009\" class=\"read-more\" href=\"http:\/\/www.majunpeng.com\/index.php\/2025\/10\/18\/%e5%9f%ba%e4%ba%8ephyloaln%e8%bf%9b%e8%a1%8c%e7%9b%b4%e7%b3%bb%e5%90%8c%e6%ba%90%e5%9f%ba%e5%9b%a0%e7%9a%84%e7%ad%9b%e9%80%89\/\" aria-label=\"\u9605\u8bfb 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