Related papers: Treewidth of display graphs: bounds, brambles and …
Treewidth is an important graph invariant, relevant for both structural and algorithmic reasons. A necessary condition for a graph class to have bounded treewidth is the absence of large cliques. We study graph classes closed under taking…
Ranked tree-child networks are a recently introduced class of rooted phylogenetic networks in which the evolutionary events represented by the network are ordered so as to respect the flow of time. This class includes the well-studied…
Phylogenies are commonly used to represent the evolutionary relationships between species, and often these phylogenies are equipped with edge lengths that indicate degrees of evolutionary difference. Given such a phylogeny, a popular…
We obtain structure theorems for graphs excluding a fan (a path with a universal vertex) or a dipole ($K_{2,k}$) as a topological minor. The corresponding decompositions can be computed in FPT linear time. This is motivated by the study of…
Phylogenetic trees elucidate evolutionary relationships among species, but phylogenetic inference remains challenging due to the complexity of combining continuous (branch lengths) and discrete parameters (tree topology). Traditional Markov…
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…
We continue the study of $(tw,\omega)$-bounded graph classes, that is, hereditary graph classes in which large treewidth is witnessed by the presence of a large clique, and the relation of this property to boundedness of the…
Phylogenomics is a new field which applies to tools in phylogenetics to genome data. Due to a new technology and increasing amount of data, we face new challenges to analyze them over a space of phylogenetic trees. Because a space of…
The notion of directed treewidth was introduced by Johnson, Robertson, Seymour and Thomas [Journal of Combinatorial Theory, Series B, Vol 82, 2001] as a first step towards an algorithmic metatheory for digraphs. They showed that some…
A rooted tree is balanced if the degree of a vertex depends only on its distance to the root. In this paper we determine the sharp threshold for the appearance of a large family of balanced spanning trees in the random geometric graph…
We present the first fixed-parameter tractable (FPT) algorithms for exact computation of generalized hypertree width (ghw) and fractional hypertree width (fhw). Our algorithms are parameterized by the target width, the rank, and the maximum…
A directed phylogenetic network is tree-child if every non-leaf vertex has a child that is not a reticulation. As a class of directed phylogenetic networks, tree-child networks are very useful from a computational perspective. For example,…
Treewidth is arguably the most important structural graph parameter leading to algorithmically beneficial graph decompositions. Triggered by a strongly growing interest in temporal networks (graphs where edge sets change over time), we…
Phylogenetic mixture models are statistical models of character evolution allowing for heterogeneity. Each of the classes in some unknown partition of the characters may evolve by different processes, or even along different trees. The…
Phylogenetic trees are leaf-labelled trees used to model the evolution of species. In practice it is not uncommon to obtain two topologically distinct trees for the same set of species, and this motivates the use of distance measures to…
Random graphs are more and more used for modeling real world networks such as evolutionary networks of proteins. For this purpose we look at two different models and analyze how properties like connectedness and degree distributions are…
Phylogenetic Diversity (PD) is a prominent quantitative measure of the biodiversity of a collection of present-day species (taxa). This measure is based on the evolutionary distance among the species in the collection. Loosely speaking, if…
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…
This work addresses the intrinsic relationship between trees and networks (i.e. graphs). A complete (invertible) mapping is presented which allows trees to be mapped into weighted graphs and then backmapped into the original tree without…
Parameterised subgraph counting problems are the most thoroughly studied topic in the theory of parameterised counting, and there has been significant recent progress in this area. Many of the existing tractability results for parameterised…