Related papers: A matroid associated with a phylogenetic tree
Semidirected networks have received interest in evolutionary biology as the appropriate generalization of unrooted trees to networks, in which some but not all edges are directed. Yet these networks lack proper theoretical study. We define…
Greedy minimum weight spanning tree packings have proven to be useful in connectivity-related problems. We study the process of greedy minimum weight base packings in general matroids and explore its applications. For general matroids, we…
It is known from the algebraic graph theory that if $L$ is the Laplacian matrix of some tree $G$ with a vertex degree sequence $\mathbf{d}=(d_1, ..., d_n)^\top$ and $D$ is its distance matrix, then…
We study an abstract notion of tree structure which lies at the common core of various tree-like discrete structures commonly used in combinatorics: trees in graphs, order trees, nested subsets of a set, tree-decompositions of graphs and…
The threshold-$k$ metric dimension ($\mathrm{Tmd}_k$) of a graph is the minimum number of sensors -- a subset of the vertex set -- needed to uniquely identify any vertex in the graph, solely based on its distances from the sensors, when the…
There are many results asserting the existence of tree-decompositions of minimal width which still represent local connectivity properties of the underlying graph, perhaps the best-known being Thomas' theorem that proves for every graph $G$…
Let T be a (not necessarily positive) weighted tree with n leaves numbered by the set {1,...,n}. Define the k-weights of the tree D_{i_1,....,i_k}(T) as the sum of the lengths of the edges of the minimal subtree connecting i_1,....,i_k. We…
The Robinson-Foulds (RF) metric is arguably the most widely used measure of phylogenetic tree similarity, despite its well-known shortcomings: For example, moving a single taxon in a tree can result in a tree that has maximum distance to…
Given a matroid M on the ground set E, the Bergman fan B(M), or space of M-ultrametrics, is a polyhedral complex in R^E which arises in several different areas, such as tropical algebraic geometry, dynamical systems, and phylogenetics.…
Let ${\cal T}=(T,w)$ be a weighted finite tree with leaves $1,..., n$.For any $I :=\{i_1,..., i_k \} \subset \{1,...,n\}$, let $D_I ({\cal T})$ be the weight of the minimal subtree of $T$ connecting $i_1,..., i_k$; the $D_{I} ({\cal T})$…
It is a classical result that any finite tree with positively weighted edges, and without vertices of degree 2, is uniquely determined by the weighted path distance between each pair of leaves. Moreover, it is possible for a (small) strict…
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.…
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…
We consider the following basic problem in phylogenetic tree construction. Let $\mathcal{P} = \{T_1, \ldots, T_k\}$ be a collection of rooted phylogenetic trees over various subsets of a set of species. The tree compatibility problem asks…
The treewidth of a graph is an important invariant in structural and algorithmic graph theory. This paper studies the treewidth of line graphs. We show that determining the treewidth of the line graph of a graph $G$ is equivalent to…
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 metric dimension of a graph $G$ is the minimal size of a subset $R$ of vertices of $G$ that, upon reporting their graph distance from a distingished (source) vertex $v^\star$, enable unique identification of the source vertex $v^\star$…
A chief problem in phylogenetics and database theory is the computation of a maximum consistent tree from a set of rooted or unrooted trees. A standard input are triplets, rooted binary trees on three leaves, or quartets, unrooted binary…
A resolving set $S$ of a graph $G$ is a subset of its vertices such that no two vertices of $G$ have the same distance vector to $S$. The Metric Dimension problem asks for a resolving set of minimum size, and in its decision form, a…
The definition of $n$-width of a bounded subset $A$ in a normed linear space $X$ is based on the existence of $n$-dimensional subspaces. Although the concept of an $n$-dimensional subspace is not available for metric trees, in this paper,…