Related papers: Reconstructing Tree-Child Networks from Reticulate…
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…
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…
Phylogenetic trees are widely used to display estimates of how groups of species evolved. Each phylogenetic tree can be seen as a collection of clusters, subgroups of the species that evolved from a common ancestor. When phylogenetic trees…
It is known that any two trees on the same $n$ leaves can be displayed by a network with $n-2$ reticulations, and there are two trees that cannot be displayed by a network with fewer reticulations. But how many reticulations are needed to…
In the context of reconstructing phylogenetic networks from a collection of phylogenetic trees, several characterisations and subsequently algorithms have been established to reconstruct a phylogenetic network that collectively embeds all…
Network reconstruction consists in retrieving the hidden interaction structure of a system from observations. Many reconstruction algorithms have been proposed, although less research has been devoted to describe their theoretical…
Invariants for complicated objects such as those arising in phylogenetics, whether they are invariants as matrices, polynomials, or other mathematical structures, are important tools for distinguishing and working with such objects. In this…
The generation of trees with a specified tree edit distance has significant applications across various fields, including computational biology, structured data analysis, and image processing. Recently, generative networks have been…
Phylogenetic networks are a generalisation of phylogenetic trees that allow for more complex evolutionary histories that include hybridisation-like processes. It is of considerable interest whether a network can be considered `tree-like' or…
We study the problem of finding a temporal hybridization network for a set of phylogenetic trees that minimizes the number of reticulations. First, we introduce an FPT algorithm for this problem on an arbitrary set of $m$ binary trees with…
The class of ranked tree-child networks, tree-child networks arising from an evolution process with a fixed embedding into the plane, has recently been introduced by Bienvenu, Lambert, and Steel. These authors derived counting results for…
Phylogenetic networks are an extension of phylogenetic trees which are used to represent evolutionary histories in which reticulation events (such as recombination and hybridization) have occurred. A central question for such networks is…
In evolutionary biology, phylogenetic networks are constructed to represent the evolution of species in which reticulate events are thought to have occurred, such as recombination and hybridization. It is therefore useful to have…
It was recently shown that a large class of phylogenetic networks, the `labellable' networks, is in bijection with the set of `expanding' covers of finite sets. In this paper, we show how several prominent classes of phylogenetic networks…
In this paper, we lay the groundwork on the comparison of phylogenetic networks based on edge contractions and expansions as edit operations, as originally proposed by Robinson and Foulds to compare trees. We prove that these operations…
Phylogenetic networks allow modeling reticulate evolution, capturing events such as hybridization and horizontal gene transfer. A fundamental computational problem in this context is the Tree Containment problem, which asks whether a given…
Tree Containment is a fundamental problem in phylogenetics useful for verifying a proposed phylogenetic network, representing the evolutionary history of certain species. Tree Containment asks whether the given phylogenetic tree (for…
A k-tree is either a complete graph on (k+1) vertices or given a k-tree G' with n vertices, a k-tree G with (n+1) vertices can be constructed by introducing a new vertex v and picking a k-clique Q in G' and then joining each vertex u in Q.…
An important problem in phylogenetics is the construction of phylogenetic trees. One way to approach this problem, known as the supertree method, involves inferring a phylogenetic tree with leaves consisting of a set $X$ of species from a…
Reconstructing the tree of life from molecular sequences is a fundamental problem in computational biology. Modern data sets often contain a large number of genes, which can complicate the reconstruction problem due to the fact that…