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Rooted phylogenetic networks are rooted acyclic digraphs. They are used to model complex evolution where hybridization, recombination and other reticulation events play important roles. A rigorous definition of network compression is introduced on the basis of the recent studies of the relationships between cluster, tree and rooted phylogenetic network. The concept reveals another interesting connection between the two well-studied network classes|tree-child networks and reticulation-visible networks|and enables us to define a new class of networks for which the cluster containment problem has a linear-time algorithm., Comment: 18 pages, 4 figures

Genetic and comparative genomic studies indicate that extant genomes are more properly considered to be a fusion product of random mutations over generations and genomic material transfers between individuals of different lineages. This has motivated researchers to adopt phylogenetic networks and other general models to study genome evolution. One important problem arising from reconstruction and verification of phylogenetic networks is the cluster containment problem, namely determining whether or not a cluster of taxa is displayed in a phylogenetic network. In this work, a new upper bound for this NP-complete problem is established through an efficient reduction to the SAT problem. Two efficient (albeit exponential time) methods are also implemented. It is developed on the basis of generalization of the so-called reticulation-visible property of phylogenetic networks., Comment: 8 figure, 19 pages

Phylogenetic networks are mathematical structures for modeling and visualization of reticulation processes in the study of evolution. Galled networks, reticulation visible networks, nearly-stable networks and stable-child networks are the four classes of phylogenetic networks that are recently introduced to study the topological and algorithmic aspects of phylogenetic networks. We prove the following results. (1) A binary galled network with n leaves has at most 2(n-1) reticulation nodes. (2) A binary nearly-stable network with n leaves has at most 3(n-1) reticulation nodes. (3) A binary stable-child network with n leaves has at most 7(n-1) reticulation nodes., Comment: 23 pages, 9 figures

In this work, we answer an open problem in the study of phylogenetic networks. Phylogenetic trees are rooted binary trees in which all edges are directed away from the root, whereas phylogenetic networks are rooted acyclic digraphs. For the purpose of evolutionary model validation, biologists often want to know whether or not a phylogenetic tree is contained in a phylogenetic network. The tree containment problem is NP-complete even for very restricted classes of networks such as tree-sibling phylogenetic networks. We prove that this problem is solvable in cubic time for stable phylogenetic networks. A linear time algorithm is also presented for the cluster containment problem., Comment: 25 pages, 3 figures

A fundamental problem in the study of phylogenetic networks is to determine whether or not a given phylogenetic network contains a given phylogenetic tree. We develop a quadratic-time algorithm for this problem for binary nearly-stable phylogenetic networks. We also show that the number of reticulations in a reticulation visible or nearly stable phylogenetic network is bounded from above by a function linear in the number of taxa., Comment: Accepted to RECOMB 2015