相关论文: Counting Phylogenetic Networks with Few Reticulati…

Phylogenetic networks extend phylogenetic trees to allow for modeling reticulate evolutionary processes such as hybridization. They take the shape of a rooted, directed, acyclic graph, and when parameterized with evolutionary parameters,…

Phylogenetic networks are rooted acyclic directed graphs in which the leaves are identified with members of a set X of species. The cluster of a vertex is the set of leaves that are descendants of the vertex. A network is "distinct-cluster"…

Given a dense triplet set $\mathcal{T}$, there arise two interesting questions: Does there exists any phylogenetic network consistent with $\mathcal{T}$? And if so, can we find an effective algorithm to construct one? For cases of networks…

In evolutionary biology, networks are becoming increasingly used to represent evolutionary histories for species that have undergone non-treelike or reticulate evolution. Such networks are essentially directed acyclic graphs with a leaf set…

Unrooted phylogenetic networks are graphs used to represent evolutionary relationships. Accurately reconstructing such networks is of great relevance for evolutionary biology. It has recently been conjectured that all phylogenetic networks…

In 2001 Allen and Steel showed that, if subtree and chain reduction rules have been applied to two unrooted phylogenetic trees, the reduced trees will have at most 28k taxa where k is the TBR (Tree Bisection and Reconnection) distance…

Semi-directed phylogenetic networks have recently emerged as a class of phylogenetic networks sitting between rooted (directed) and unrooted (undirected) phylogenetic networks as they contain both directed as well as undirected edges. While…

Phylogenetic networks are becoming increasingly popular in phylogenetics since they have the ability to describe a wider range of evolutionary events than their tree counterparts. In this paper, we study Markov models on phylogenetic…

In this paper we enumerate and give bijections for the following four sets of vertices among rooted ordered trees of a fixed size: (i) first-children of degree $k$ at level $\ell$, (ii) non-first-children of degree $k$ at level $\ell-1$,…

Phylogenetic networks are a generalization of evolutionary trees that are used by biologists to represent the evolution of organisms which have undergone reticulate evolution. Essentially, a phylogenetic network is a directed acyclic graph…

Phylogenetic networks are useful in representing the evolutionary history of taxa. In certain scenarios, one requires a way to compare different networks. In practice, this can be rather difficult, except within specific classes of…

Recently, so-called treebased phylogenetic networks have gained considerable interest in the literature, where a treebased network is a network that can be constructed from a phylogenetic tree, called the base tree, by adding additional…

Phylogenetic networks model reticulate evolutionary histories. The last two decades have seen an increased interest in establishing mathematical results and developing computational methods for inferring and analyzing these networks. A…

Let $X$ be a finite set, $\mathcal N$ be a reticulation-visible network on $X$, and $\mathcal T$ be a rooted binary phylogenetic tree. We show that there is a polynomial-time algorithm for deciding whether or not $\mathcal N$ displays…

In mathematical phylogenetics, evolutionary relationships are often represented by trees and networks. The latter are typically used whenever the relationships cannot be adequately described by a tree, which happens when so-called…

Here we show that, given a set of clusters C on a set of taxa X, where |X|=n, it is possible to determine in time f(k).poly(n) whether there exists a level-<= k network (i.e. a network where each biconnected component has reticulation…

In evolutionary biology, phylogenetic networks are graphs that provide a flexible framework for representing complex evolutionary histories that involve reticulate evolutionary events. Recently phylogenetic studies have started to focus on…

Many real networks have cliques as their constitutional units. Here we present a family of scale-free network model consist of cliques, which is established by a simple recursive algorithm. We investigate the networks both analytically and…

Phylogenetic networks are increasingly used in evolutionary biology to represent the history of species that have undergone reticulate events such as horizontal gene transfer, hybrid speciation and recombination. One of the most fundamental…

Many classes of phylogenetic networks have been proposed in the literature. A feature of several of these classes is that if one restricts a network in the class to a subset of its leaves, then the resulting network may no longer lie within…