{"title":"TreeRefiner:一种在系统发育树上精炼多重比对的工具。","authors":"Aswath Manohar, Serafim Batzoglou","doi":"10.1109/csb.2005.53","DOIUrl":null,"url":null,"abstract":"<p><p>We present TreeRefiner, a tool for refining multiple alignments of biological sequences. Given a multiple alignment, a phylogenetic tree, and scoring parameters as input, TreeRefiner optimizes the sum-of-pairs function in a restricted three-dimensional space around the alignment. At each internal node of the unrooted tree, the multiple alignment is projected to the sub-alignments corresponding to the three neighboring nodes, and three-dimensional dynamic programming is performed within a user-specified radius r around the original alignment. We test TreeRefiner on simulated sequences aligned by several popular tools, and demonstrate substantial improvements in the percentage of correctly aligned positions.</p>","PeriodicalId":87417,"journal":{"name":"Proceedings. IEEE Computational Systems Bioinformatics Conference","volume":" ","pages":"111-9"},"PeriodicalIF":0.0000,"publicationDate":"2005-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1109/csb.2005.53","citationCount":"3","resultStr":"{\"title\":\"TreeRefiner: a tool for refining a multiple alignment on a phylogenetic tree.\",\"authors\":\"Aswath Manohar, Serafim Batzoglou\",\"doi\":\"10.1109/csb.2005.53\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><p>We present TreeRefiner, a tool for refining multiple alignments of biological sequences. Given a multiple alignment, a phylogenetic tree, and scoring parameters as input, TreeRefiner optimizes the sum-of-pairs function in a restricted three-dimensional space around the alignment. At each internal node of the unrooted tree, the multiple alignment is projected to the sub-alignments corresponding to the three neighboring nodes, and three-dimensional dynamic programming is performed within a user-specified radius r around the original alignment. We test TreeRefiner on simulated sequences aligned by several popular tools, and demonstrate substantial improvements in the percentage of correctly aligned positions.</p>\",\"PeriodicalId\":87417,\"journal\":{\"name\":\"Proceedings. IEEE Computational Systems Bioinformatics Conference\",\"volume\":\" \",\"pages\":\"111-9\"},\"PeriodicalIF\":0.0000,\"publicationDate\":\"2005-01-01\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://sci-hub-pdf.com/10.1109/csb.2005.53\",\"citationCount\":\"3\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Proceedings. IEEE Computational Systems Bioinformatics Conference\",\"FirstCategoryId\":\"1085\",\"ListUrlMain\":\"https://doi.org/10.1109/csb.2005.53\",\"RegionNum\":0,\"RegionCategory\":null,\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"\",\"JCRName\":\"\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Proceedings. IEEE Computational Systems Bioinformatics Conference","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.1109/csb.2005.53","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"","JCRName":"","Score":null,"Total":0}
TreeRefiner: a tool for refining a multiple alignment on a phylogenetic tree.
We present TreeRefiner, a tool for refining multiple alignments of biological sequences. Given a multiple alignment, a phylogenetic tree, and scoring parameters as input, TreeRefiner optimizes the sum-of-pairs function in a restricted three-dimensional space around the alignment. At each internal node of the unrooted tree, the multiple alignment is projected to the sub-alignments corresponding to the three neighboring nodes, and three-dimensional dynamic programming is performed within a user-specified radius r around the original alignment. We test TreeRefiner on simulated sequences aligned by several popular tools, and demonstrate substantial improvements in the percentage of correctly aligned positions.
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