article

Mixed Integer Linear Programming for Maximum-Parsimony Phylogeny Inference

Authors:

Srinath Sridhar,

Guy E. Blelloch,

Russell SchwartzAuthors Info & Claims

IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB), Volume 5, Issue 3

Pages 323 - 331

https://doi.org/10.1109/TCBB.2008.26

Published: 01 July 2008 Publication History

Abstract

Reconstruction of phylogenetic trees is a fundamental problem in computational biology. While excellent heuristic methods are available for many variants of this problem, new advances in phylogeny inference will be required if we are to be able to continue to make effective use of the rapidly growing stores of variation data now being gathered. In this paper, we present two integer linear programming (ILP) formulations to find the most parsimonious phylogenetic tree from a set of binary variation data. One method uses a flow-based formulation that can produce exponential numbers of variables and constraints in the worst case. The method has, however, proven extremely efficient in practice on datasets that are well beyond the reach of the available provably efficient methods, solving several large mtDNA and Y-chromosome instances within a few seconds and giving provably optimal results in times competitive with fast heuristics than cannot guarantee optimality. An alternative formulation establishes that the problem can be solved with a polynomial-sized ILP. We further present a web server developed based on the exponential-sized ILP that performs fast maximum parsimony inferences and serves as a front end to a database of precomputed phylogenies spanning the human genome.

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Cited By

Deepak ADong JFernández-Baca D(2012)Identifying rogue taxa through reduced consensusProceedings of the 8th international conference on Bioinformatics Research and Applications10.1007/978-3-642-30191-9_9(87-98)Online publication date: 21-May-2012
https://dl.acm.org/doi/10.1007/978-3-642-30191-9_9
Dong JFernández-Baca DMcMorris F(2009)Constructing majority-rule supertreesProceedings of the 9th international conference on Algorithms in bioinformatics10.5555/1812906.1812913(73-84)Online publication date: 12-Sep-2009
https://dl.acm.org/doi/10.5555/1812906.1812913

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Published In

cover image IEEE/ACM Transactions on Computational Biology and Bioinformatics

IEEE/ACM Transactions on Computational Biology and Bioinformatics Volume 5, Issue 3

July 2008

159 pages

ISSN:1545-5963

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IEEE Computer Society Press

Washington, DC, United States

Publication History

Published: 01 July 2008

Published in TCBB Volume 5, Issue 3

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Cited By

Deepak ADong JFernández-Baca D(2012)Identifying rogue taxa through reduced consensusProceedings of the 8th international conference on Bioinformatics Research and Applications10.1007/978-3-642-30191-9_9(87-98)Online publication date: 21-May-2012
https://dl.acm.org/doi/10.1007/978-3-642-30191-9_9
Dong JFernández-Baca DMcMorris F(2009)Constructing majority-rule supertreesProceedings of the 9th international conference on Algorithms in bioinformatics10.5555/1812906.1812913(73-84)Online publication date: 12-Sep-2009
https://dl.acm.org/doi/10.5555/1812906.1812913

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