Reconstructing Phylogenetic Level-1 Networks from Nondense Binet and Trinet Sets

Binets and trinets are phylogenetic networks with two and three leaves, respectively. Here we consider the problem of deciding if there exists a binary level-1 phylogenetic network displaying a given set  T of binary binets or trinets over a taxon set  X , and constructing such a network whenever it...

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Veröffentlicht in:Algorithmica Jg. 77; H. 1; S. 173 - 200
Hauptverfasser: Huber, Katharina T., van Iersel, Leo, Moulton, Vincent, Scornavacca, Celine, Wu, Taoyang
Format: Journal Article
Sprache:Englisch
Veröffentlicht: New York Springer US 01.01.2017
Springer Nature B.V
Springer Verlag
Schlagworte:
Algorithm Analysis and Problem Complexity
Algorithms
Bioinformatics
Computer Science
Computer Systems Organization and Communication Networks
Data Structures and Information Theory
Mathematics of Computing
Networks
Phylogenetics
Polynomials
Theory of Computation
Phylogenetic network
NP-hard
Supernetwork
Phylogenetic tree
Exponential-time algorithm
Polynomial-time algorithm
Trinet
Aho algorithm
ISSN:0178-4617, 1432-0541
Online-Zugang:Volltext
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Zusammenfassung:Binets and trinets are phylogenetic networks with two and three leaves, respectively. Here we consider the problem of deciding if there exists a binary level-1 phylogenetic network displaying a given set  T of binary binets or trinets over a taxon set  X , and constructing such a network whenever it exists. We show that this is NP-hard for trinets but polynomial-time solvable for binets. Moreover, we show that the problem is still polynomial-time solvable for inputs consisting of binets and trinets as long as the cycles in the trinets have size three. Finally, we present an  O ( 3 | X | p o l y ( | X | ) ) time algorithm for general sets of binets and trinets. The latter two algorithms generalise to instances containing level-1 networks with arbitrarily many leaves, and thus provide some of the first supernetwork algorithms for computing networks from a set of rooted phylogenetic networks.
Bibliographie:ObjectType-Article-1
SourceType-Scholarly Journals-1
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content type line 14
ISSN:0178-4617
1432-0541
DOI:10.1007/s00453-015-0069-8