Related papers: The median of the distance between two leaves in a…
The need for structures capable of accommodating complex evolutionary signals such as those found in, for example, wheat has fueled research into phylogenetic networks. Such structures generalize the standard phylogenetic tree model by also…
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 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…
The search for similarity and dissimilarity measures on phylogenetic trees has been motivated by the computation of consensus trees, the search by similarity in phylogenetic databases, and the assessment of clustering results in…
A phylogenetic tree shows the evolutionary relationships among species. Internal nodes of the tree represent speciation events and leaf nodes correspond to species. A goal of phylogenetics is to combine such trees into larger trees, called…
In this paper, we lay the groundwork on the comparison of phylogenetic networks based on edge contractions and expansions as edit operations, as originally proposed by Robinson and Foulds to compare trees. We prove that these operations…
Many classes of phylogenetic networks have been proposed in the literature. A feature of several of these classes is that if one restricts a network in the class to a subset of its leaves, then the resulting network may no longer lie within…
A (pseudo-)metric $D$ on a finite set $X$ is said to be a `tree metric' if there is a finite tree with leaf set $X$ and non-negative edge weights so that, for all $x,y \in X$, $D(x,y)$ is the path distance in the tree between $x$ and $y$.…
Given a Galton-Watson process conditioned to have total progeny equal to $n$, we study the asymptotic probability that this conditioned Galton-Watson process has distance to the border bigger or equal than $k$, as the number of nodes $n…
Let $\mathcal{T}$ be the set of spanning trees of $G$ and let $L(T)$ be the number of leaves in a tree $T$. The leaf number $L(G)$ of $G$ is defined as $L(G)=\max\{L(T)|T\in \mathcal{T}\}$. Let $G$ be a connected graph of order $n$ and…
Within the field of phylogenetics there is great interest in distance measures to quantify the dissimilarity of two trees. Here, based on an idea of Bruen and Bryant, we propose and analyze a new distance measure: the Maximum Parsimony (MP)…
A phylogenetic tree is an acyclic graph with distinctly labeled leaves, whose internal edges have a positive weight. Given a set of n leaves, the collection of all phylogenetic trees with this leaf set can be assembled into a metric cube…
Ultametrics are an important class of distances used in applications such as phylogenetics, clustering and classification theory. Ultrametrics are essentially distances that can be represented by an edge-weighted rooted tree so that all of…
Phylogenetic trees summarize evolutionary relationships between organisms, and tools to analyze collections of phylogenetic trees enable contrasts between different genes' ancestry. The BHV metric space has enabled the analysis of…
We provide a logarithmic upper bound for the disentangling number on unordered lists of leaf labeled trees. This results is useful for analyzing phylogenetic mixture models. The proof depends on interpreting multisets of trees as high…
Trees with labelled leaves and with all other vertices of degree three play an important role in systematic biology and other areas of classification. A classical combinatorial result ensures that such trees can be uniquely reconstructed…
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…
Unrooted phylogenetic networks are graphs used to represent evolutionary relationships. Accurately reconstructing such networks is of great relevance for evolutionary biology. It has recently been conjectured that all phylogenetic networks…
The classic Maxwell formula calculates the length of a planar locally minimal binary tree in terms of coordinates of its boundary vertices and directions of incoming edges. However, if an extreme tree with a given topology and a boundary…
We study the average leaf-to-leaf path lengths on ordered Catalan tree graphs with $n$ nodes and show that these are equivalent to the average length of paths starting from the root node. We give an explicit analytic formula for the average…