Kernelizations for the hybridization number problem on multiple nonbinary trees

Given a finite set X, a collection T of rooted phylogenetic trees on X and an integer k, the Hybridization Number problem asks if there exists a phylogenetic network on X that displays all trees from T and has reticulation number at most k. We show two kernelization algorithms for Hybridization Numb...

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Vydáno v:Journal of computer and system sciences Ročník 82; číslo 6; s. 1075 - 1089
Hlavní autoři: van Iersel, Leo, Kelk, Steven, Scornavacca, Celine
Médium: Journal Article
Jazyk:angličtina
Vydáno: Elsevier Inc 01.09.2016
Elsevier
Témata:
Algorithms
Bioinformatics
Collection
Computer Science
Computer simulation
Displays
Fixed-parameter tractability
Hybridization number
Kernelization
Kernels
Mathematical analysis
Mathematical models
Phylogenetic network
Phylogenetic tree
Trees
Hybridization number
Phylogenetic network
Fixed-parameter tractability
Phylogenetic tree
Kernelization
phylogenetic network
phylogenetic tree
hybridization number
kernelization
ISSN:0022-0000, 1090-2724
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Popis
Shrnutí:Given a finite set X, a collection T of rooted phylogenetic trees on X and an integer k, the Hybridization Number problem asks if there exists a phylogenetic network on X that displays all trees from T and has reticulation number at most k. We show two kernelization algorithms for Hybridization Number, with kernel sizes 4k(5k)t and 20k2(Δ+−1) respectively, with t the number of input trees and Δ+ their maximum outdegree. Experiments on simulated data demonstrate the practical relevance of our kernelization algorithms. In addition, we present an nf(k)t-time algorithm, with n=|X| and f some computable function of k. •We study constructing a network displaying a given collection of phylogenetic trees.•Our kernelization techniques work for inputs consisting of multiple binary trees.•Previous results were restricted to two trees and/or binary trees.•A unified and simplified approach for dealing with common chains of nonbinary trees.•Polynomial-time solvability with fixed number of reticulations.
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ISSN:0022-0000
1090-2724
DOI:10.1016/j.jcss.2016.03.006