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

Aswath Manohar; Serafim Batzoglou

doi:10.1109/csb.2005.53

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

Aswath Manohar·Serafim Batzoglou

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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 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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Algorithms Animals Base Sequence Chromosome Mapping Humans Molecular Sequence Data Phylogeny Sequence Alignment Sequence Analysis, DNA Software Evaluation Study Journal Article Research Support, U.S. Gov't, Non-P.H.S.

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Aswath Manohar, Serafim Batzoglou. 2005. TreeRefiner: a tool for refining a multiple alignment on a phylogenetic tree.. https://doi.org/10.1109/csb.2005.53

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