A Simple Fixed Parameter Tractable Algorithm for Computing the Hybridization Number of Two (Not Necessarily Binary) Trees

Here, we present a new fixed parameter tractable algorithm to compute the hybridization number r of two rooted, not necessarily binary phylogenetic trees on taxon set X in time (6 r r!) · poly(n), where n = |X|. The novelty of this approach is its use of terminals, which are maximal elements of a na...

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Bibliographic Details
Published in:IEEE/ACM transactions on computational biology and bioinformatics Vol. 10; no. 1; pp. 18 - 25
Main Authors: Piovesan, Teresa, Kelk, Steven M.
Format: Journal Article
Language:English
Published: United States IEEE 01.01.2013
The Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subjects:
Algorithms
Bioinformatics
Cluster Analysis
Clustering algorithms
Computational biology
Computational Biology - methods
fixed parameter tractability
Hybridization, Genetic
nonbinary
Phylogenetic network
Phylogeny
Polynomials
Silicon
Vegetation
ISSN:1545-5963, 1557-9964, 1557-9964
Online Access:Get full text
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Summary:Here, we present a new fixed parameter tractable algorithm to compute the hybridization number r of two rooted, not necessarily binary phylogenetic trees on taxon set X in time (6 r r!) · poly(n), where n = |X|. The novelty of this approach is its use of terminals, which are maximal elements of a natural partial order on X, and several insights from the softwired clusters literature. This yields a surprisingly simple and practical bounded-search algorithm and offers an alternative perspective on the underlying combinatorial structure of the hybridization number problem.
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ISSN:1545-5963
1557-9964
1557-9964
DOI:10.1109/TCBB.2012.134