Related papers: Normalising phylogenetic networks
Phylogenetic networks are directed acyclic graphs that depict the genomic evolution of related taxa. Reticulation nodes in such networks (nodes with more than one parent) represent reticulate evolutionary events, such as recombination,…
Phylogenetic networks provide a means of describing the evolutionary history of sets of species believed to have undergone hybridization or gene flow during their evolution. The mutation process for a set of such species can be modeled as a…
Phylogenetic networks are a generalization of evolutionary or phylogenetic trees that are commonly used to represent the evolution of species which cross with one another. A special type of phylogenetic network is an {\em $X$-cactus}, which…
We provide precise asymptotic estimates for the number of general phylogenetic networks by using analytic combinatorial methods. Recently, this approach is studied by Fuchs, Gittenberger, and the author himself (Australasian Journal of…
Phylogenetic networks are a type of leaf-labelled, acyclic, directed graph used by biologists to represent the evolutionary history of species whose past includes reticulation events. A phylogenetic network is tree-child if each non-leaf…
In the study of rooted phylogenetic networks, analyzing the set of rooted phylogenetic trees that are embedded in such a network is a recurring task. From an algorithmic viewpoint, this analysis almost always requires an exhaustive search…
The need for structures capable of accommodating complex evolutionary signals such as those found in, for example, wheat has fueled research into phylogenetic networks. Such structures generalize the standard phylogenetic tree model by also…
The inference of phylogenetic networks, which model complex evolutionary processes including hybridization and gene flow, remains a central challenge in evolutionary biology. Until now, statistically consistent inference methods have been…
One strategy for reconstruction of phylogenetic networks is to solve the phylogenetic network problem, which involves inferring phylogenetic trees first and subsequently computing the smallest phylogenetic network that displays all the…
In phylogenetics, evolution is traditionally represented in a tree-like manner. However, phylogenetic networks can be more appropriate for representing evolutionary events such as hybridization, horizontal gene transfer, and others. In…
Phylogenetic networks are graphs that are used to represent evolutionary relationships between different taxa. They generalize phylogenetic trees since for example, unlike trees, they permit lineages to combine. Recently, there has been…
Phylogenetic networks generalize evolutionary trees, and are commonly used to represent evolutionary histories of species that undergo reticulate evolutionary processes such as hybridization, recombination and lateral gene transfer.…
Phylogenetic networks and, more generally, directed acyclic graphs (DAGs) represent hierarchical structure beyond trees, for instance in the presence of reticulate evolutionary events such as hybridization or horizontal gene transfer. A…
Structural information of phylogenetic tree topologies plays an important role in phylogenetic inference. However, finding appropriate topological structures for specific phylogenetic inference tasks often requires significant design effort…
The evolution of molecular and phenotypic traits is commonly modelled using Markov processes along a phylogeny. This phylogeny can be a tree, or a network if it includes reticulations, representing events such as hybridization or admixture.…
Phylogenetic networks are a generalization of phylogenetic trees to leaf-labeled directed acyclic graphs that represent ancestral relationships between species whose past includes non-tree-like events such as hybridization and horizontal…
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"…
A binary phylogenetic network may or may not be obtainable from a tree by the addition of directed edges (arcs) between tree arcs. Here, we establish a precise and easily tested criterion (based on `2-SAT') that efficiently determines…
Phylogenetic networks provide a framework for representing evolutionary histories involving reticulate events such as hybridization or horizontal gene transfer. A central problem is to infer such networks from local structural information.…
Phylogenetic networks are rooted, labelled directed acyclic graphs which are commonly used to represent reticulate evolution. There is a close relationship between phylogenetic networks and multi-labelled trees (MUL-trees). Indeed, any…