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The probability that two randomly selected phylogenetic trees of the same size are isomorphic is found to be asymptotic to a decreasing exponential modulated by a polynomial factor. The number of symmetrical nodes in a random phylogenetic…
We consider the following basic problem in phylogenetic tree construction. Let $\mathcal{P} = \{T_1, \ldots, T_k\}$ be a collection of rooted phylogenetic trees over various subsets of a set of species. The tree compatibility problem asks…
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…
Graphs are interesting structures: extremely useful to depict real-life problems, extremely easy to understand given a sketch, extremely complicated to represent formally, extremely complicated to compare. Phylogeny is the study of the…
It is well-known that the height profile of a critical conditioned Galton-Watson tree with finite offspring variance converges, after a suitable normalization, to the local time of a standard Brownian excursion. In this work, we study the…
A rooted tree is balanced if the degree of a vertex depends only on its distance to the root. In this paper we determine the sharp threshold for the appearance of a large family of balanced spanning trees in the random geometric graph…
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…
There exists a bijection between one stack sortable permutations --permutations which avoid the pattern 231-- and planar trees. We define an edit distance between permutations which is coherent with the standard edit distance between trees.…
We present two algorithms for computing the geodesic distance between phylogenetic trees in tree space, as introduced by Billera, Holmes, and Vogtmann (2001). We show that the possible combinatorial types of shortest paths between two trees…
An important problem in geometric computing is defining and computing similarity between two geometric shapes, e.g. point sets, curves and surfaces, etc. Important geometric and topological information of many shapes can be captured by…
Galled trees, directed acyclic graphs that model evolutionary histories with isolated hybridization events, have become very popular due to both their biological significance and the existence of polynomial time algorithms for their…
Consider the complete graph on $n$ vertices, with edge weights drawn independently from the exponential distribution with unit mean. Janson showed that the typical distance between two vertices scales as $\log{n}/n$, whereas the diameter…
Phylogenetic networks are a generalization of phylogenetic trees that allow for representation of reticulate evolution. Recently, a space of unrooted phylogenetic networks was introduced, where such a network is a connected graph in which…
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…
Due to hybridization events in evolution, studying two different genes of a set of species may yield two related but different phylogenetic trees for the set of species. In this case, we want to measure the dissimilarity of the two trees.…
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…
In this article, we propose tree edit distance with variables, which is an extension of the tree edit distance to handle trees with variables and has a potential application to measuring the similarity between mathematical formulas,…
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 study the problem of computing the diameter and the mean distance of a continuous graph, i.e., a connected graph where all points along the edges, instead of only the vertices, must be taken into account. It is known that for continuous…
Agreement forests continue to play a central role in the comparison of phylogenetic trees since their introduction more than 25 years ago. More specifically, they are used to characterise several distances that are based on tree…