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A Simple Fixed Parameter Tractable Algorithm for Computing the Hybridization Number of Two (Not Necessarily Binary) Trees
Jan.-Feb. 2013 (vol. 10 no. 1)
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
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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