TreeRefiner：一种用于在系统发育树上优化多重比对的工具。

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

作者信息

Manohar Aswath, Batzoglou Serafim

机构信息

Department of Computer Science, Stanford University, CA 94305, USA.

出版信息

Proc IEEE Comput Syst Bioinform Conf. 2005:111-9. doi: 10.1109/csb.2005.53.

DOI:10.1109/csb.2005.53

PMID:16447969

Abstract

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.

摘要

我们展示了TreeRefiner，一种用于优化生物序列多序列比对的工具。给定一个多序列比对、一棵系统发育树和评分参数作为输入，TreeRefiner在比对周围的受限三维空间中优化双序列和函数。在无根树的每个内部节点，多序列比对被投影到与三个相邻节点对应的子比对上，并在围绕原始比对的用户指定半径r内执行三维动态规划。我们在由几种流行工具比对的模拟序列上测试了TreeRefiner，并证明了正确比对位置的百分比有显著提高。