Related papers: Planar Rooted Phylogenetic Networks
The problem of constructing an optimal rooted phylogenetic network from a set of rooted triplets is an NP-hard problem. In this paper, we present a heuristic algorithm called TripNet which tries to construct an optimal rooted phylogenetic…
A phylogenetic network is a simplex (or 1-component tree-child) network if the child of every reticulation node is a network leaf. Simplex networks are a superclass of phylogenetic trees and a subclass of tree-child networks. Generalizing…
We compare the phylogenetic tensors for various trees and networks for two, three and four taxa. If the probability spaces between one tree or network and another are not identical then there will be phylogenetic tensors that could have…
We study the enumeration of spinal tree-child phylogenetic networks, a rigid family of tree-child networks in which all internal vertices lie on a single root--to--leaf path. We provide two complementary combinatorial frameworks. First, we…
For a phylogenetic tree, the phylogenetic diversity of a set A of taxa is the total weight of edges on paths to A. Finding small sets of maximal diversity is crucial for conservation planning, as it indicates where limited resources can be…
Bayesian networks faithfully represent the symmetric conditional independences existing between the components of a random vector. Staged trees are an extension of Bayesian networks for categorical random vectors whose graph represents…
Tree-child networks, one of the prominent network classes in phylogenetics, have been introduced for the purpose of modeling reticulate evolution. Recently, the first author together with Gittenberger and Mansouri (2019) showed that the…
Phylogenetic trees represent certain species and their likely ancestors. In such a tree, present-day species are leaves and an edge from u to v indicates that u is an ancestor of v. Weights on these edges indicate the phylogenetic distance.…
A network $N$ on a finite set $X$, $|X|\geq 2$, is a connected directed acyclic graph with leaf set $X$ in which every root in $N$ has outdegree at least 2 and no vertex in $N$ has indegree and outdegree equal to 1; $N$ is arboreal if the…
Two new classes of networks are introduced that resemble small-world properties. These networks are recursively constructed but retain a fixed, regular degree. They consist of a one-dimensional lattice backbone overlayed by a hierarchical…
The comprehensive characterization of the structure of complex networks is essential to understand the dynamical processes which guide their evolution. The discovery of the scale-free distribution and the small world property of real…
The Rooted Maps Theory, a branch of the Theory of Homology, is shown to be a powerful tool for investigating the topological properties of Feynman diagrams, related to the single particle propagator in the quantum many-body systems. The…
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.…
The study of network representations of physical, biological, and social phenomena can help us better understand the structural and functional dynamics of their networks and formulate predictive models of these phenomena. However, due to…
Trees have long been used as a graphical representation of species relationships. However complex evolutionary events, such as genetic reassortments or hybrid speciations which occur commonly in viruses, bacteria and plants, do not fit into…
Given a rooted, binary phylogenetic network and a rooted, binary phylogenetic tree, can the tree be embedded into the network? This problem, called \textsc{Tree Containment}, arises when validating networks constructed by phylogenetic…
A tanglegram consists of two rooted binary trees and a perfect matching between their leaves, and a planar tanglegram is one that admits a layout with no crossings. We show that the problem of generating planar tanglegrams uniformly at…
We introduce a biologically natural, mathematically tractable model of random phylogenetic network to describe evolution in the presence of hybridization. One of the features of this model is that the hybridization rate of the lineages…
When hybridization or other forms of lateral gene transfer have occurred, evolutionary relationships of species are better represented by phylogenetic networks than by trees. While inference of such networks remains challenging, several…
We introduce some natural families of distributions on rooted binary ranked plane trees with a view toward unifying ideas from various fields, including macroevolution, epidemiology, computational group theory, search algorithms and other…