Related papers: Note on expected internode distances for gene tree…
It is common in phylogenetics to have some, perhaps partial, information about the overall evolutionary tree of a group of organisms and wish to find an evolutionary tree of a specific gene for those organisms. There may not be enough…
Optimal transport provides a metric which quantifies the dissimilarity between probability measures. For measures supported in discrete metric spaces, finding the optimal transport distance has cubic time complexity in the size of the…
Networks are ubiquitous in biology and computational approaches have been largely investigated for their inference. In particular, supervised machine learning methods can be used to complete a partially known network by integrating various…
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…
We establish maximal trees and graphs for the difference of average distance and proximity proving thus the corresponding conjecture posed in [4]. We also establish maximal trees for the difference of average eccentricity and remoteness and…
Topology of exponential and scale-free trees and simple graphs is investigated numerically. The numbers of the nearest neighbors, the next-nearest neighbors, the next-next-nearest neighbors, the 4-th and the 5-th neighbors are calculated.…
A classical result, fundamental to evolutionary biology, states that an edge-weighted tree $T$ with leaf set $X$, positive edge weights, and no vertices of degree 2 can be uniquely reconstructed from the set of leaf-to-leaf distances…
Given two binary trees on $N$ labeled leaves, the quartet distance between the trees is the number of disagreeing quartets. By permuting the leaves at random, the expected quartets distance between the two trees is…
Species tree estimation from multi-locus datasets is statistically challenging for multiple reasons, including gene tree heterogeneity across the genome due to incomplete lineage sorting (ILS). Species tree estimation methods have been…
It has been claimed in Aldous, Miermont and Pitman [PTRF, 2004] that all L\'evy trees are mixings of inhomogeneous continuum random trees. We give a rigorous proof of this claim in the case of a stable branching mechanism, relying on a new…
We study the number of distance queries needed to identify certain properties of a hidden tree $T$ on $n$ vertices. A distance query consists of two vertices $x,y$, and the answer is the distance of $x$ and $y$ in $T$. We determine the…
An $r$-matching in a graph $G$ is a collection of edges in $G$ such that the distance between any two edges is at least $r$. A $2$-matching is also called an induced matching. In this paper, we estimate the maximum number of $r$-matchings…
Consider a rooted tree $T$ with leaf-set $[n]$, and with all non-leaf vertices having out-degree $2$, at least. A rooted tree $\mathcal T$ with leaf-set $S\subset [n]$ is induced by $S$ in $T$ if $\mathcal T$ is the lowest common ancestor…
It is proposed that the co-expression of statistically significant motifs among the sequences of a proteome is a phylogenetic trait. From the co-expression matrix of such motifs in a group of prokaryotic proteomes a suitable definition of a…
A method was developed for Bayesian inference of species phylogeny using the multi-species coalescent model. To improve the mixing properties of the Markov chain Monte Carlo (MCMC) algorithm that traverses the space of species trees, we…
In this paper, we present a flexible and probabilistic framework for tracking topological features in time-varying scalar fields using merge trees and partial optimal transport. Merge trees are topological descriptors that record the…
Phylogenetic networks are used to represent the evolutionary history of species. Recently, the new class of orchard networks was introduced, which were later shown to be interpretable as trees with additional horizontal arcs. This makes the…
The status of a vertex $x$ in a graph is the sum of the distances between $x$ and all other vertices. Let $G$ be a connected graph. The status sequence of $G$ is the list of the statuses of all vertices arranged in nondecreasing order. $G$…
The ongoing explosion of genome sequence data is transforming how we reconstruct and understand the histories of biological systems. Across biological scales, from individual cells to populations and species, trees-based models provide a…
Inferential summaries of tree estimates are useful in the setting of evolutionary biology, where phylogenetic trees have been built from DNA data since the 1960's. In bioinformatics, psychometrics and data mining, hierarchical clustering…