Related papers: Treewidth distance on phylogenetic trees
Phylogenetic networks generalise phylogenetic trees and allow for the accurate representation of the evolutionary history of a set of present-day species whose past includes reticulate events such as hybridisation and lateral gene transfer.…
In phylogenetics, distances are often used to measure the incongruence between a pair of phylogenetic trees that are reconstructed by different methods or using different regions of genome. Motivated by the maximum parsimony principle in…
The recently introduced graph parameter tree-cut width plays a similar role with respect to immersions as the graph parameter treewidth plays with respect to minors. In this paper, we provide the first algorithmic applications of tree-cut…
Phylogenetic networks are a type of directed acyclic graph that represent how a set $X$ of present-day species are descended from a common ancestor by processes of speciation and reticulate evolution. In the absence of reticulate evolution,…
The twin-width of a graph measures its distance to co-graphs and generalizes classical width concepts such as tree-width or rank-width. Since its introduction in 2020 (Bonnet et. al. 2020), a mass of new results has appeared relating twin…
We prove that the tree-width of graphs in a hereditary class defined by a finite set $F$ of forbidden induced subgraphs is bounded if and only if $F$ includes a complete graph, a complete bipartite graph, a tripod (a forest in which every…
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 are leaf-labelled trees used to model the evolution of species. Here we explore the practical impact of kernelization (i.e. data reduction) on the NP-hard problem of computing the TBR distance between two unrooted binary…
Structural parameters of graphs, such as treewidth, play a central role in the study of the parameterized complexity of graph problems. Motivated by the study of parametrized algorithms on phylogenetic networks, scanwidth was introduced…
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…
The notion of treewidth, introduced by Robertson and Seymour in their seminal Graph Minors series, turned out to have tremendous impact on graph algorithmics. Many hard computational problems on graphs turn out to be efficiently solvable in…
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…
We describe a kernel of size 9k-8 for the NP-hard problem of computing the Tree Bisection and Reconnect (TBR) distance k between two unrooted binary phylogenetic trees. We achieve this by extending the existing portfolio of reduction rules…
Phylogenetic networks are a generalization of phylogenetic trees that allow for the representation of non-treelike evolutionary events, like recombination, hybridization, or lateral gene transfer. In this paper, we present and study a new…
Phylogenetic networks are used to represent the evolutionary history of species. They are versatile when compared to traditional phylogenetic trees, as they capture more complex evolutionary events such as hybridization and horizontal gene…
Dynamic graph theory is a novel, growing area that deals with graphs that change over time and is of great utility in modelling modern wireless, mobile and dynamic environments. As a graph evolves, possibly arbitrarily, it is challenging to…
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 \emph{matching} is a subset of edges in a graph $G$ that do not share an endpoint. A matching $M$ is a \emph{$\mathcal{P}$-matching} if the subgraph of $G$ induced by the endpoints of the edges of $M$ satisfies property $\mathcal{P}$. For…
We prove that the (divisorial) gonality of a finite connected graph is lower bounded by its treewidth. We show that equality holds for grid graphs and complete multipartite graphs. We prove that the treewidth lower bound also holds for…
Deciding whether there is a single tree -a supertree- that summarizes the evolutionary information in a collection of unrooted trees is a fundamental problem in phylogenetics. We consider two versions of this question: agreement and…