Related papers: Three-way symbolic tree-maps and ultrametrics

A metric phylogenetic tree relating a collection of taxa induces weighted rooted triples and weighted quartets for all subsets of three and four taxa, respectively. New intertaxon distances are defined that can be calculated from these…

A trivalent diagram is a connected, two-colored bipartite graph (parallel edges allowed but not loops) such that every black vertex is of degree 1 or 3 and every white vertex is of degree 1 or 2, with a cyclic order imposed on every set of…

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.…

We introduce the tree distance, a new distance measure on graphs. The tree distance can be computed in polynomial time with standard methods from convex optimization. It is based on the notion of fractional isomorphism, a characterization…

Given two messages - as linear sequences of letters, it is immediate to determine whether one can be transformed into the other by simple substitution cipher of the letters. On the other hand, if the letters are carried as labels on nodes…

We review the theory and practice of determining what parts of a data set are ultrametric. It is assumed that the data set, to begin with, is endowed with a metric, and we include discussion of how this can be brought about if a…

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…

A digraph is connected-homogeneous if any isomorphism between finite connected induced subdigraphs extends to an automorphism of the digraph. We consider locally-finite connected-homogeneous digraphs with more than one end. In the case that…

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…

Phylogenetic networks extend phylogenetic trees to model non-vertical inheritance, by which a lineage inherits material from multiple parents. The computational complexity of estimating phylogenetic networks from genome-wide data with…

Large tree structures are ubiquitous and real-world relational datasets often have information associated with nodes (e.g., labels or other attributes) and edges (e.g., weights or distances) that need to be communicated to the viewers. Yet,…

We generalize the concept of ascending and descending runs from permutations to rooted labelled trees and mappings, i.e., functions from the set $\{1, \dots, n\}$ into itself. A combinatorial decomposition of the corresponding functional…

This paper presents and explores a theory of \emph{multiholomorphic maps}. This group of ideas generalizes the theory of pseudoholomorphic curves in a direction suggested by consideration of the kinds of compatible geometric structures that…

We consider three probability measures on subsets of edges of a given finite graph $G$, namely those which govern, respectively, a uniform forest, a uniform spanning tree, and a uniform connected subgraph. A conjecture concerning the…

We give a short and direct proof of a remarkable identity that arises in the enumeration of labeled trees with respect to their indegree sequence, where all edges are oriented from the vertex with lower label towards the vertex with higher…

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 prove identifiability of the tree parameters of the 3-class Jukes-Cantor mixture model. The proof uses ideas from algebraic statistics, in particular: finding phylogenetic invariants that separate the varieties associated to different…

Tree alignment graphs (TAGs) provide an intuitive data structure for storing phylogenetic trees that exhibits the relationships of the individual input trees and can potentially account for nested taxonomic relationships. This paper…

We introduce bijections between families of rooted maps with unfixed genus and families of so-called blossoming trees endowed with an arbitrary forward matching of their leaves. We first focus on Eulerian maps with controlled vertex…

The inducibility of a graph represents its maximum density as an induced subgraph over all possible sequences of graphs of size growing to infinity. This invariant of graphs has been extensively studied since its introduction in $1975$ by…