Related papers: The median of the distance between two leaves in a…
The tree-metric theorem provides a necessary and sufficient condition for a dissimilarity matrix to be a tree metric, and has served as the foundation for numerous distance-based reconstruction methods in phylogenetics. Our main result is…
Tree comparison metrics have proven to be an invaluable aide in the reconstruction and analysis of phylogenetic (evolutionary) trees. The path-length distance between trees is a particularly attractive measure as it reflects differences in…
In this work we study the interleaving distance between merge trees from a combinatorial point of view. We use a particular type of matching between trees to obtain a novel formulation of the distance. With such formulation, we tackle the…
Given two phylogenetic trees with the $\{1, \ldots, n\}$ leaf-set the maximum agreement subtree problem asks what is the maximum size of the subset $A \subseteq \{1, \ldots, n\}$ such that the two trees are equivalent when restricted to…
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.…
In this paper we investigate an extremal problem on binary phylogenetic trees. Given two such trees $T_1$ and $T_2$, both with leaf-set ${1,2,...,n}$, we are interested in the size of the largest subset $S \subseteq {1,2,...,n}$ of leaves…
We show that the expected size of the maximum agreement subtree of two $n$-leaf trees, uniformly random among all trees with the shape, is $\Theta(\sqrt{n})$. To derive the lower bound, we prove a global structural result on a decomposition…
In phylogenetic networks, it is desirable to estimate edge lengths in substitutions per site or calendar time. Yet, there is a lack of scalable methods that provide such estimates. Here we consider the problem of obtaining edge length…
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 trees are leaf-labelled trees, where the leaves correspond to extant species (taxa), and the internal vertices represent ancestral species. The evolutionary history of a set of species can be explained by more than one…
The interleaving distance is a key tool for comparing merge trees, which provide topological summaries of scalar functions. In this work, we define an average merge tree for a pair of merge trees using the interleaving distance. Since such…
Let $L(n,d)$ denote the minimum possible number of leaves in a tree of order $n$ and diameter $d.$ In 1975 Lesniak gave the lower bound $B(n,d)=\lceil 2(n-1)/d\rceil$ for $L(n,d).$ When $d$ is even, $B(n,d)=L(n,d).$ But when $d$ is odd,…
We study distorted metrics on binary trees in the context of phylogenetic reconstruction. Given a binary tree $T$ on $n$ leaves with a path metric $d$, consider the pairwise distances $\{d(u,v)\}$ between leaves. It is well known that these…
Let $T$ be an arbitrary phylogenetic tree with $n$ leaves. It is well-known that the average quartet distance between two assignments of taxa to the leaves of $T$ is $\frac 23 \binom{n}{4}$. However, a longstanding conjecture of Bandelt and…
The early development of a zygote can be mathematically described by a developmental tree. To compare developmental trees of different species, we need to define distances on trees. If children cells after a division are not…
The asymmetric tropical distance is a distance measure on the tropical torus $\mathbb{R}^n/\mathbb{R}\mathbf{1}$ and in particular on the Bergman fan $B(K_N) \subseteq \mathbb{R}^{\binom{N}{2}}/\mathbb{R}\mathbf{1}$ of the complete…
We consider spanning trees of $n$ points in convex position whose edges are pairwise non-crossing. Applying a flip to such a tree consists in adding an edge and removing another so that the result is still a non-crossing spanning tree.…
Phylogenetic trees are frequently used to model evolution. Such trees are typically reconstructed from data like DNA, RNA, or protein alignments using methods based on criteria like maximum parsimony (amongst others). Maximum parsimony has…
It follows from a classical result of Jordan that every tree with maximum degree at most $r$ containing a vertex set labeled by $[n]$, has a single-edge cut which separates two subsets $A,B \subset [n]$ for which $\min\{|A|,|B|\} \ge…
Billey et al. [arXiv:1507.04976] have recently discovered a surprisingly simple formula for the number $a_n(\sigma)$ of leaf-labelled rooted non-embedded binary trees (also known as phylogenetic trees) with $n\geq 1$ leaves, fixed (for the…