TreeRefiner: A tool for refining a multiple alignment on a phylogenetic tree

被引：3
|
作者：
Manohar, A [1 ]
Batzoglou, S [1 ]
机构：
[1] Stanford Univ, Dept Comp Sci, Stanford, CA 94305 USA
来源：
2005 IEEE COMPUTATIONAL SYSTEMS BIOINFORMATICS CONFERENCE, PROCEEDINGS | 2005年
关键词：
D O I：
10.1109/CSB.2005.53
中图分类号：
Q81 [生物工程学（生物技术）]; Q93 [微生物学];
学科分类号：
071005 ; 0836 ; 090102 ; 100705 ;
摘要：
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.
引用
收藏
页码：111 / 119
页数：9
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