Related papers: Treewidth distance on phylogenetic trees
We prove that if every subgraph of a graph $G$ has a balanced separation of order at most $a$ then $G$ has treewidth at most $15a$. This establishes a linear dependence between the treewidth and the separation number.
We discuss a notion of convergence for binary trees that is based on subtree sizes. In analogy to recent developments in the theory of graphs, posets and permutations we investigate some general aspects of the topology, such as a…
Reduced parameters [BKW, JCTB '26; BKRT, SODA '22] are defined via contraction sequences. Based on this framework, we introduce the reduced component max-leaf, denoted by $\operatorname{cml}^\downarrow$, where component max-leaf is the…
Inspired by the interval decomposition of persistence modules and the extended Newick format of phylogenetic networks, we show that, inside the larger category of \textit{ordered Reeb graphs}, every Reeb graph with $n$ leaves and first…
Treewidth and hypertree width have proven to be highly successful structural parameters in the context of the Constraint Satisfaction Problem (CSP). When either of these parameters is bounded by a constant, then CSP becomes solvable in…
Understanding the evolution of a set of genes or species is a fundamental problem in evolutionary biology. The problem we study here takes as input a set of trees describing {possibly discordant} evolutionary scenarios for a given set of…
Parameterized complexity seeks to use input structure to obtain faster algorithms for NP-hard problems. This has been most successful for graphs of low treewidth: Many problems admit fast algorithms relative to treewidth and many of them…
Maximum parsimony distance is a measure used to quantify the dissimilarity of two unrooted phylogenetic trees. It is NP-hard to compute, and very few positive algorithmic results are known due to its complex combinatorial structure. Here we…
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…
Consider a drawing of a graph $G$ in the plane such that crossing edges are coloured differently. The minimum number of colours, taken over all drawings of $G$, is the classical graph parameter "thickness". By restricting the edges to be…
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 this paper we propose, implement, and test the first practical decomposition algorithms for the width parameters treecut width and treedepth. These two parameters have recently gained a lot of attention in the theoretical research…
For a given graph G and integers b,f >= 0, let S be a subset of vertices of G of size b+1 such that the subgraph of G induced by S is connected and S can be separated from other vertices of G by removing f vertices. We prove that every…
In this work, we answer an open problem in the study of phylogenetic networks. Phylogenetic trees are rooted binary trees in which all edges are directed away from the root, whereas phylogenetic networks are rooted acyclic digraphs. For the…
We present a class of linear programming approximations for constrained optimization problems. In the case of mixed-integer polynomial optimization problems, if the intersection graph of the constraints has bounded tree-width our…
We consider bounded width CNF-formulas where the width is measured by popular graph width measures on graphs associated to CNF-formulas. Such restricted graph classes, in particular those of bounded treewidth, have been extensively studied…
Rotation distances measure the differences in structure between rooted ordered binary trees. The one-dimensional skeleta of associahedra are rotation graphs, where two vertices representing trees are connected by an edge if they differ by a…
Twin-width is a structural width parameter introduced by Bonnet, Kim, Thomass\'e and Watrigant [FOCS 2020]. Very briefly, its essence is a gradual reduction (a contraction sequence) of the given graph down to a single vertex while…
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…
Phylogenetic networks are used to represent evolutionary scenarios in biology and linguistics. To find the most probable scenario, it may be necessary to compare candidate networks, to distinguish different networks, and to see when one…