A Practical Fixed-Parameter Algorithm for Constructing Tree-Child Networks from Multiple Binary Trees

We present the first fixed-parameter algorithm for constructing a tree-child phylogenetic network that displays an arbitrary number of binary input trees and has the minimum number of reticulations among all such networks. The algorithm uses the recently introduced framework of cherry picking sequen...

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Vydáno v:	Algorithmica Ročník 84; číslo 4; s. 917 - 960
Hlavní autoři:	van Iersel, Leo, Janssen, Remie, Jones, Mark, Murakami, Yukihiro, Zeh, Norbert
Médium:	Journal Article
Jazyk:	angličtina
Vydáno:	New York Springer US 01.04.2022 Springer Nature B.V
Témata:	Algorithm Analysis and Problem Complexity Algorithms Computer Science Computer Systems Organization and Communication Networks Data Structures and Information Theory Mathematics of Computing Parameters Personal computers Phylogenetics Theory of Computation Phylogenetic networks Hybridization number Fixed-parameter algorithms
ISSN:	0178-4617, 1432-0541
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Abstract	We present the first fixed-parameter algorithm for constructing a tree-child phylogenetic network that displays an arbitrary number of binary input trees and has the minimum number of reticulations among all such networks. The algorithm uses the recently introduced framework of cherry picking sequences and runs in O ( ( 8 k ) k poly ( n , t ) ) time, where n is the number of leaves of every tree, t is the number of trees, and k is the reticulation number of the constructed network. Moreover, we provide an efficient parallel implementation of the algorithm and show that it can deal with up to 100 input trees on a standard desktop computer, thereby providing a major improvement over previous phylogenetic network construction methods.
AbstractList	We present the first fixed-parameter algorithm for constructing a tree-child phylogenetic network that displays an arbitrary number of binary input trees and has the minimum number of reticulations among all such networks. The algorithm uses the recently introduced framework of cherry picking sequences and runs in O ( ( 8 k ) k poly ( n , t ) ) time, where n is the number of leaves of every tree, t is the number of trees, and k is the reticulation number of the constructed network. Moreover, we provide an efficient parallel implementation of the algorithm and show that it can deal with up to 100 input trees on a standard desktop computer, thereby providing a major improvement over previous phylogenetic network construction methods. We present the first fixed-parameter algorithm for constructing a tree-child phylogenetic network that displays an arbitrary number of binary input trees and has the minimum number of reticulations among all such networks. The algorithm uses the recently introduced framework of cherry picking sequences and runs in O((8k)kpoly(n,t)) time, where n is the number of leaves of every tree, t is the number of trees, and k is the reticulation number of the constructed network. Moreover, we provide an efficient parallel implementation of the algorithm and show that it can deal with up to 100 input trees on a standard desktop computer, thereby providing a major improvement over previous phylogenetic network construction methods.
Author	Janssen, Remie van Iersel, Leo Jones, Mark Zeh, Norbert Murakami, Yukihiro
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Cites_doi	10.1109/TCBB.2011.137 10.1093/bioinformatics/btq198 10.1016/j.jcss.2016.03.006 10.1016/j.ipl.2013.02.010 10.1007/s11538-013-9874-x 10.1080/10635150500431197 10.1186/s12859-015-0660-7 10.1109/TCBB.2015.2462336 10.1007/s00285-005-0315-9 10.1177/117693430700300017 10.1137/110845045 10.1093/sysbio/syu023 10.1109/tcbb.2007.1019 10.1007/s00026-011-0108-3 10.1137/15M1036579 10.1186/1745-6150-6-34 10.1016/j.aam.2019.01.004
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SubjectTerms	Algorithm Analysis and Problem Complexity Algorithms Computer Science Computer Systems Organization and Communication Networks Data Structures and Information Theory Mathematics of Computing Parameters Personal computers Phylogenetics Theory of Computation
Title	A Practical Fixed-Parameter Algorithm for Constructing Tree-Child Networks from Multiple Binary Trees
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