2004
DOI: 10.1142/s0219720004000521
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Optimal, Efficient Reconstruction of Phylogenetic Networks With Constrained Recombination

Abstract: A phylogenetic network is a generalization of a phylogenetic tree, allowing structural properties that are not tree-like. In a seminal paper, Wang et al.(1) studied the problem of constructing a phylogenetic network, allowing recombination between sequences, with the constraint that the resulting cycles must be disjoint. We call such a phylogenetic network a "galled-tree". They gave a polynomial-time algorithm that was intended to determine whether or not a set of sequences could be generated on galled-tree. U… Show more

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Cited by 163 publications
(176 citation statements)
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“…Wang et al then considered a restricted problem in which all recombination events are associated with nodedisjoint recombination cycles. Gusfield et al (2004a) gave necessary and sufficient conditions to identify these networks, which they called ''galled-trees,'' and they added a much more specific and realistic model of recombination events. Gusfield et al (2004b) gave a more detailed study of these node-disjoint cycles.…”
Section: Introductionmentioning
confidence: 99%
“…Wang et al then considered a restricted problem in which all recombination events are associated with nodedisjoint recombination cycles. Gusfield et al (2004a) gave necessary and sufficient conditions to identify these networks, which they called ''galled-trees,'' and they added a much more specific and realistic model of recombination events. Gusfield et al (2004b) gave a more detailed study of these node-disjoint cycles.…”
Section: Introductionmentioning
confidence: 99%
“…2 below). This type of network was first considered in [20] and is closely related to so-called galled-trees [3,7]. Level-1 networks have been used to, for example, analyse virus evolution [10], and are of practical importance since their simple structure allows for efficient construction [7,10,15] and comparison [17].…”
Section: Introductionmentioning
confidence: 99%
“…They then consider a restricted problem in which all recombination events are associated with node-disjoint recombination cycles, and they present a sufficient condition to identify such networks. Gusfield et al [2] give necessary and sufficient conditions to identify these networks, which they call "galled-trees," and they add a much more specific and realistic model of recombination events. In [3] they give a more detailed study of these node-disjoint cycles.…”
Section: Introductionmentioning
confidence: 99%
“…Thus, for extant taxa u and v we typically assume a distance d(u, v) that measures the evolutionary change between u and v. Like Wang et al [15] and Gusfield et al [2] this paper models only the case of binary characters in rooted acyclic directed graphs. Unlike [15] and [2] we shall assume that the network itself is given. We then study the problem of inferring complete distance information (such as all the branch lengths) within the network.…”
Section: Introductionmentioning
confidence: 99%