Related papers: A matroid associated with a phylogenetic tree

The \emph{distance matrix} of a simple connected graph $G$ is $D(G)=(d_{ij})$, where $d_{ij}$ is the distance between the vertices $i$ and $j$ in $G$. We consider a weighted tree $T$ on $n$ vertices with edge weights are square matrix of…

The classical matrix tree theorem relates the number of spanning trees of a connected graph with the product of the nonzero eigenvalues of its Laplacian matrix. The class of regular matroids generalizes that of graphical matroids, and a…

We define an independence system associated with simple graphs. We prove that the independence system is a matroid for certain families of graphs, including trees, with bases as minimal resolving sets. Consequently, the greedy algorithm on…

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…

We introduce the notion of metric semilattice on the metric space and prove the criterion of $\R$-tree as connected geodesic metric space $X$ admitting the partial order, such that $X$ is semilinear metric semilattice. Also we state the…

Given a distance matrix consisting of pairwise distances between species, a distance-based phylogenetic reconstruction method returns a tree metric or equidistant tree metric (ultrametric) that best fits the data. We investigate…

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…

It is known that PQ-symmetric maps on the boundary characterize the quasi-isometry type of visual hyperbolic spaces, in particular, of geodesically complete \br-trees. We define a map on pairs of PQ-symmetric ultrametric spaces which…

Let $T$ be a tree with vertex set $\{1, \ldots, n\}$ such that each edge is assigned a nonzero weight. The squared distance matrix of $T,$ denoted by $\Delta,$ is the $n \times n$ matrix with $(i,j)$-element $d(i,j)^2,$ where $d(i,j)$ is…

In Francis and Steel (2015), it was shown that there exists non-trivial networks on $4$ leaves upon which the distance metric affords a metric on a tree which is not the base tree of the network. In this paper we extend this result in two…

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…

We investigate the tractability of a simple fusion of two fundamental structures on graphs, a spanning tree and a perfect matching. Specifically, we consider the following problem: given an edge-weighted graph, find a minimum-weight…

Three-way dissimilarities are a generalization of (two-way) dissimilarities which can be used to indicate the lack of homogeneity or resemblance between any three objects. Such maps have applications in cluster analysis, and have been used…

A metric tree ($M$, $d$), also known as $\mathbb{R}$-trees or $T$-theory, is a metric space such that between any two points there is an unique arc and that arc is isometric to an interval in $\mathbb{R}$. In this paper after presenting…

Phylogenetic networks are a generalisation of phylogenetic trees that allow for more complex evolutionary histories that include hybridisation-like processes. It is of considerable interest whether a network can be considered `tree-like' or…

Let $T$ be a weighted tree. The weight of a subtree $T_1$ of $T$ is defined as the product of weights of vertices and edges of $T_1$. We obtain a linear-time algorithm to count the sum of weights of subtrees of $T$. As applications, we…

We consider the class of graphs for which the edge connectivity is equal to the maximum number of edge-disjoint spanning trees, and the natural generalization to matroids, where the cogirth is equal to the number of disjoint bases. We…

Treewidth is a graph parameter that plays a fundamental role in several structural and algorithmic results. We study the problem of decomposing a given graph $G$ into node-disjoint subgraphs, where each subgraph has sufficiently large…

Topological phylogenetic trees can be assigned edge weights in several natural ways, highlighting different aspects of the tree. Here the rooted triple and quartet metrizations are introduced, and applied to formulate novel fast methods of…

Let T=(V,E) be a tree graph with non-negative weights defined on the vertices. A vertex z is called a separating vertex for u and v if the distances of z to u and v are not equal. A set of vertices L\subseteq V is a feasible solution for…