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

被引:23
|
作者
Huber, Katharina T. [1 ]
van Iersel, Leo [2 ]
Moulton, Vincent [1 ]
Scornavacca, Celine [3 ,4 ]
Wu, Taoyang [1 ]
机构
[1] Univ East Anglia, Sch Comp Sci, Norwich, Norfolk, England
[2] Delft Univ Technol, Delft Inst Appl Math, Delft, Netherlands
[3] Univ Montpellier, CNRS, ISEM, Montpellier, France
[4] Inst Biol Computat, Montpellier, France
关键词
Phylogenetic tree; Phylogenetic network; Polynomial-time algorithm; Exponential-time algorithm; NP-hard; Supernetwork; Trinet; Aho algorithm; ROOTED TRIPLETS; TREES;
D O I
10.1007/s00453-015-0069-8
中图分类号
TP31 [计算机软件];
学科分类号
081202 ; 0835 ;
摘要
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(vertical bar X vertical bar) poly(vertical bar X vertical bar)) 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.
引用
收藏
页码:173 / 200
页数:28
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