Related papers: A matroid associated with a phylogenetic tree
We consider random binary trees that appear as the output of certain standard algorithms for sorting and searching if the input is random. We introduce the subtree size metric on search trees and show that the resulting metric spaces…
A binary phylogenetic network may or may not be obtainable from a tree by the addition of directed edges (arcs) between tree arcs. Here, we establish a precise and easily tested criterion (based on `2-SAT') that efficiently determines…
This paper studies the "explanation problem" for tree- and linearly-ordered array data, a problem motivated by database applications and recently solved for the one-dimensional tree-ordered case. In this paper, one is given a matrix A whose…
Given a tree of weighted vertices, it is sometimes possible to break the tree into two equally-weighted subtrees within an allowable error. We give a fast algorithm that finds an edge which breaks the tree into equal-weight components or…
We consider the numerical taxonomy problem of fitting a positive distance function ${D:{S\choose 2}\rightarrow \mathbb R_{>0}}$ by a tree metric. We want a tree $T$ with positive edge weights and including $S$ among the vertices so that…
Compatibility of unrooted phylogenetic trees is a well studied problem in phylogenetics. It asks to determine whether for a set of k input trees there exists a larger tree (called a supertree) that contains the topologies of all k input…
We revisit the issue of low-distortion embedding of metric spaces into the line, and more generally, into the shortest path metric of trees, from the parameterized complexity perspective.Let $M=M(G)$ be the shortest path metric of an edge…
The Laplacian matrix of a graph $G$ is $L(G)=D(G)-A(G)$, where $A(G)$ is the adjacency matrix and $D(G)$ is the diagonal matrix of vertex degrees. According to the Matrix-Tree Theorem, the number of spanning trees in $G$ is equal to any…
It is folklore that tree-width is monotone under taking subgraphs (i.e. injective graph homomorphisms) and contractions (certain kinds of surjective graph homomorphisms). However, although tree-width is obviously not monotone under any…
Consider a collection of points in the plane and the sets of slopes or directions of the lines between pairs of points. It is known that the algebraic matroid on the set of direction constraints between the points is equivalent to the…
Null models of binary phylogenetic trees are useful for testing hypotheses on real world phylogenies. In this paper we consider phylogenies as binary trees without edge lengths together with a sampling measure and encode them as algebraic…
Hlineny's Theorem shows that any sentence in the monadic second-order logic of matroids can be tested in polynomial time, when the input is limited to a class of F-representable matroids with bounded branch-width (where F is a finite…
Metric embeddings are central to metric theory and its applications. Here we consider embeddings of a different sort: maps from a set to subsets of a metric space so that distances between points are approximated by minimal distances…
Let $D$ be a connected weighted digraph. The relation between the vertex weighted complexity (with a fixed root) of the line digraph of $D$ and the edge weighted complexity (with a fixed root) of $D$ has been given in (L. Levine, Sandpile…
The necessary and sufficient conditions under which a given family $\mathcal{F}$ of subsets of finite set $X$ coincides with the family $\mathbf{B}_X$ of all balls generated by some ultrametric $d$ on $X$ are found. It is shown that the…
Given a rooted, binary phylogenetic network and a rooted, binary phylogenetic tree, can the tree be embedded into the network? This problem, called \textsc{Tree Containment}, arises when validating networks constructed by phylogenetic…
For a fixed set $X$, an arbitrary \textit{weight structure} $d \in [0,\infty]^{X \times X}$ can be interpreted as a distance assignment between pairs of points on $X$. Restrictions (i.e. \textit{metric axioms}) on the behaviour of any such…
In phylogenetics, a central problem is to infer the evolutionary relationships between a set of species $X$; these relationships are often depicted via a phylogenetic tree -- a tree having its leaves univocally labeled by elements of $X$…
We compare three basic kinds of discrete mathematical models used to portray phylogenetic relationships among species and higher taxa: phylogenetic trees, Hennig trees and Nelson cladograms. All three models are trees, as that term is…
A geophylogeny is a phylogenetic tree (or dendrogram) where each leaf (e.g. biological taxon) has an associated geographic location (site). To clearly visualize a geophylogeny, the tree is typically represented as a crossing-free drawing…