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 sumof-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.

• Type: Conference
• Year: 2005
• Where: CSB
• Authors: Aswath Manohar, Serafim Batzoglou
• Keywords: Bioinformatics, CSB 2005, Multiple Alignment, Original Alignment, Three-dimensional Dynamic Programming