TreeRefiner: A Tool for Refining a Multiple Alignment on a Phylogenetic Tree

Authors:
Aswath Manohar;Serafim Batzoglou
Affiliations:
Stanford University;Stanford University
Venue:
CSB '05 Proceedings of the 2005 IEEE Computational Systems Bioinformatics Conference
Year:
2005

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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 thesum-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.