Related papers: Average-Tree Phylogenetic Diversity Parameterized …

We show that the eccentricities, diameter, radius, and Wiener index of an undirected $n$-vertex graph with nonnegative edge lengths can be computed in time $O(n\cdot \binom{k+\lceil\log n\rceil}{k} \cdot 2^k k^2 \log n)$, where $k$ is the…

A common problem in phylogenetics is to try to infer a species phylogeny from gene trees. We consider different variants of this problem. The first variant, called Unrestricted Minimal Episodes Inference, aims at inferring a species tree…

We introduce a new phylogenetic reconstruction algorithm which, unlike most previous rigorous inference techniques, does not rely on assumptions regarding the branch lengths or the depth of the tree. The algorithm returns a forest which is…

There are several tools available to infer phylogenetic trees, which depict the evolutionary relationships among biological entities such as viral and bacterial strains in infectious outbreaks, or cancerous cells in tumor progression trees.…

Phylogenetic network is an evolutionary model that uses a rooted directed acyclic graph (instead of a tree) to model an evolutionary history of species in which reticulate events (e.g., hybrid speciation or horizontal gene transfer)…

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…

In this paper we compare and illustrate the algorithmic use of graphs of bounded tree-width and graphs of bounded clique-width. For this purpose we give polynomial time algorithms for computing the four basic graph parameters independence…

We identify a sufficient condition, treewidth-pliability, that gives a polynomial-time algorithm for an arbitrarily good approximation of the optimal value in a large class of Max-2-CSPs parameterised by the class of allowed constraint…

This paper studies the relationship between undirected (unrooted) and directed (rooted) phylogenetic networks. We describe a polynomial-time algorithm for deciding whether an undirected nonbinary phylogenetic network, given the locations of…

We show an $\widetilde{O}(m^{1.5} \epsilon^{-1})$ time algorithm that on a graph with $m$ edges and $n$ vertices outputs its spanning tree count up to a multiplicative $(1+\epsilon)$ factor with high probability, improving on the previous…

Phylogenetic trees are leaf-labelled trees, where the leaves correspond to extant species (taxa), and the internal vertices represent ancestral species. The evolutionary history of a set of species can be explained by more than one…

Phylogenetic networks are becoming of increasing interest to evolutionary biologists due to their ability to capture complex non-treelike evolutionary processes. From a combinatorial point of view, such networks are certain types of rooted…

A large class of phylogenetic networks can be obtained from trees by the addition of horizontal edges between the tree edges. These networks are called tree based networks. Reticulation-visible networks and child-sibling networks are all…

We investigate a relaxation of the notion of fractional treewidth-fragility, namely fractional tree-independence-number-fragility. In particular, we obtain polynomial-time approximation schemes for meta-problems such as finding a…

Recently, so-called treebased phylogenetic networks have gained considerable interest in the literature, where a treebased network is a network that can be constructed from a phylogenetic tree, called the base tree, by adding additional…

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…

Treedepth is a central parameter to algorithmic graph theory. The current state-of-the-art in computing and approximating treedepth consists of a $2^{O(k^2)} n$-time exact algorithm and a polynomial-time $O(\text{OPT} \log^{3/2}…

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…

We address an open question of Francis and Steel about phylogenetic networks and trees. They give a polynomial time algorithm to decide if a phylogenetic network, N, is tree-based and pose the problem: given a fixed tree T and network N, is…

Phylogenetic networks are necessary to represent the tree of life expanded by edges to represent events such as horizontal gene transfers, hybridizations or gene flow. Not all species follow the paradigm of vertical inheritance of their…