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TreeRefiner: A Tool for Refining a Multiple Alignment on a Phylogenetic Tree
Stanford, California August 08-August 11
DOI Bookmark: http://doi.ieeecomputersociety.org/10.1109/CSB.2005.532005 IEEE Computational Systems Bioin ...
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Aswath Manohar, Serafim Batzoglou, "TreeRefiner: A Tool for Refining a Multiple Alignment on a Phylogenetic Tree," Computational Systems Bioinformatics Conference, International IEEE Computer Society, pp. 111-119, 2005 IEEE Computational Systems Bioinformatics Conference (CSB'05), 2005.
 
 
BibTex
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@article{ 10.1109/CSB.2005.53,
author = {Aswath Manohar and Serafim Batzoglou},
title = {TreeRefiner: A Tool for Refining a Multiple Alignment on a Phylogenetic Tree},
journal ={Computational Systems Bioinformatics Conference, International IEEE Computer Society},
volume = {0},
year = {2005},
isbn = {0-7695-2344-7},
pages = {111-119},
doi = {http://doi.ieeecomputersociety.org/10.1109/CSB.2005.53},
publisher = {IEEE Computer Society},
address = {Los Alamitos, CA, USA},
}
 
 
RefWorks Procite/RefMan/Endnote
x 
 
TY - CONF
JO - Computational Systems Bioinformatics Conference, International IEEE Computer Society
TI - TreeRefiner: A Tool for Refining a Multiple Alignment on a Phylogenetic Tree
SN - 0-7695-2344-7
SP111
EP119
A1 - Aswath Manohar,
A1 - Serafim Batzoglou,
PY - 2005
KW - null
VL - 0
JA - Computational Systems Bioinformatics Conference, International IEEE Computer Society
ER -
 
Aswath Manohar, Stanford University
Serafim Batzoglou, Stanford University
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.
Citation:
Aswath Manohar, Serafim Batzoglou, "TreeRefiner: A Tool for Refining a Multiple Alignment on a Phylogenetic Tree," csb, pp.111-119, 2005 IEEE Computational Systems Bioinformatics Conference (CSB'05), 2005
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