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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Shrnutí: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.
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ISSN:0178-4617
1432-0541
DOI:10.1007/s00453-021-00914-8