Related papers: On low treewidth graphs and supertrees
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…
In computational phylogenetics, the problem of constructing a supertree of a given set of rooted input trees can be formalized in different ways, to cope with contradictory information in the input. We consider the Minimum Flip Supertree…
The Subtree Isomorphism problem asks whether a given tree is contained in another given tree. The problem is of fundamental importance and has been studied since the 1960s. For some variants, e.g., ordered trees, near-linear time algorithms…
The notion of $\mathcal{H}$-treewidth, where $\mathcal{H}$ is a hereditary graph class, was recently introduced as a generalization of the treewidth of an undirected graph. Roughly speaking, a graph of $\mathcal{H}$-treewidth at most $k$…
The Maximum Agreement Forest (Maf) problem is a well-studied problem in evolutionary biology, which asks for a largest common subforest of a given collection of phylogenetic trees with identical leaf label-set. However, the previous work…
Phylogenetic (evolutionary) trees and networks are leaf-labeled graphs that are widely used to represent the evolutionary relationships between entities such as species, languages, cancer cells, and viruses. To reconstruct and analyze…
Phylogenetic networks are a generalization of phylogenetic trees that are used to represent non-tree-like evolutionary histories that arise in organisms such as plants and bacteria, or uncertainty in evolutionary histories. An…
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…
The phylogenetic tree construction is to infer the evolutionary relationship between species from the experimental data. However, the experimental data are often imperfect and conflicting each others. Therefore, it is important to extract…
Let $G$ be an undirected graph. We say that $G$ contains a ladder of length $k$ if the $2 \times (k+1)$ grid graph is an induced subgraph of $G$ that is only connected to the rest of $G$ via its four cornerpoints. We prove that if all the…
Tree-based phylogenetic networks, which may be roughly defined as leaf-labeled networks built by adding arcs only between the original tree edges, have elegant properties for modeling evolutionary histories. We answer an open question of…
The overlap graphs of subtrees in a tree (SOGs) generalise many other graphs classes with set representation characterisations. The complexity of recognising SOGs in open. The complexities of recognising many subclasses of SOGs are known.…
The maximum modularity of a graph is a parameter widely used to describe the level of clustering or community structure in a network. Determining the maximum modularity of a graph is known to be NP-complete in general, and in practice a…
We consider combinatorial problems that can be solved in polynomial time for graphs of bounded treewidth but where the order of the polynomial that bounds the running time is expected to depend on the treewidth bound. First we review some…
Given a set of leaf-labeled trees with identical leaf sets, the well-known "Maximum Agreement SubTree" problem (MAST) consists of finding a subtree homeomorphically included in all input trees and with the largest number of leaves. Its…
For a graph property $\Pi$, Subgraph Complementation to $\Pi$ is the problem to find whether there is a subset $S$ of vertices of the input graph $G$ such that modifying $G$ by complementing the subgraph induced by $S$ results in a graph…
The notion of treewidth plays an important role in theoretical and practical studies of graph problems. It has been recognized that, especially in practical environments, when computing the treewidth of a graph it is invaluable to first…
For a given graph $G$, a depth-first search (DFS) tree $T$ of $G$ is an $r$-rooted spanning tree such that every edge of $G$ is either an edge of $T$ or is between a \textit{descendant} and an \textit{ancestor} in $T$. A graph $G$ together…
Semi-labeled trees are phylogenies whose internal nodes may be labeled by higher-order taxa. Thus, a leaf labeled Mus musculus could nest within a subtree whose root node is labeled Rodentia, which itself could nest within a subtree whose…
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…