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Issue No.01 - Jan.-Feb. (2013 vol.10)
pp: 18-25
Teresa Piovesan , Dept. of Knowledge Eng. (DKE), Maastricht Univ., Maastricht, Netherlands
Steven M. Kelk , Dept. of Knowledge Eng. (DKE), Maastricht Univ., Maastricht, Netherlands
ABSTRACT
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 (6rr!) · 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.
INDEX TERMS
Vegetation, Phylogeny, Clustering algorithms, Polynomials, Silicon, Computational biology, Bioinformatics,nonbinary, Phylogenetic network, fixed parameter tractability
CITATION
Teresa Piovesan, Steven M. Kelk, "A Simple Fixed Parameter Tractable Algorithm for Computing the Hybridization Number of Two (Not Necessarily Binary) Trees", IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol.10, no. 1, pp. 18-25, Jan.-Feb. 2013, doi:10.1109/TCBB.2012.134
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