Related papers: The space of equidistant phylogenetic cactuses

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…

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.…

It is known that PQ-symmetric maps on the boundary characterize the quasi-isometry type of visual hyperbolic spaces, in particular, of geodesically complete \br-trees. We define a map on pairs of PQ-symmetric ultrametric spaces which…

We study the geometry of metrics and convexity structures on the space of phylogenetic trees, which is here realized as the tropical linear space of all \ ultrametrics. The ${\rm CAT}(0)$-metric of Billera-Holmes-Vogtman arises from the…

The metric space of phylogenetic trees defined by Billera, Holmes, and Vogtmann, which we refer to as BHV space, provides a natural geometric setting for describing collections of trees on the same set of taxa. However, it is sometimes…

In evolutionary biology, phylogenetic networks are now widely used to represent the historical relationships between species and population, when this history includes reticulation events such as hybridization, gene flow and admixture…

An infinite dimensional notion of asymptotic structure is considered. This notion is developed in terms of trees and branches on Banach spaces. Every countably infinite countably branching tree $\mathcal T$ of a certain type on a space X is…

Ultrametric matrices are a class of covariance matrices that arise in latent tree models. As a parameter space in a statistical model, the set of ultrametric matrices is neither convex nor a smooth manifold. Focus in the literature has…

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…

Computational inference of dated evolutionary histories relies upon various hypotheses about RNA, DNA, and protein sequence mutation rates. Using mutation rates to infer these dated histories is referred to as molecular clock assumption.…

For $d\ge 2$ and an odd prime power $q$, consider the vector space $\mathbb{F}_q^d$ over the finite field $\mathbb{F}_q$, where the distance between two points $(x_1,\ldots,x_d)$ and $(y_1,\ldots,y_d)$ is defined as $\sum_{i=1}^d…

Metrics on rooted phylogenetic trees are integral to a number of areas of phylogenetic analysis. Cluster-similarity metrics have recently been introduced in order to limit skew in the distribution of distances, and to ensure that trees in…

The reliability of a phylogenetic inference method from genomic sequence data is ensured by its statistical consistency. Bayesian inference methods produce a sample of phylogenetic trees from the posterior distribution given sequence data.…

We study quasiisometric embeddings between finite-dimensional CAT(0) cube complexes. More specifically, we introduce geometric branching conditions under which flats in the domain, not necessarily of top rank, are mapped within finite…

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…

Phylogenetic networks which are, as opposed to trees, suitable to describe processes like hybridization and horizontal gene transfer, play a substantial role in evolutionary research. However, while non-treelike events need to be taken into…

Rooted bifurcating trees are mathematical objects used to model evolutionary relationships and arise naturally in both coalescent theory and phylogenetics. Recent numerical representations of tree topologies, known as F-matrices, allow for…

An important and well-studied problem in phylogenetics is to compute a \emph{consensus tree} so as to summarize the common features within a collection of rooted phylogenetic trees, all whose leaf-sets are bijectively labeled by the same…

An Euclidean greedy embedding of a graph is a straight-line embedding in the plane, such that for every pair of vertices $s$ and $t$, the vertex $s$ has a neighbor $v$ with smaller distance to $t$ than $s$. This drawing style is motivated…

Dissimilarity measures for (possibly weighted) phylogenetic trees based on the comparison of their vectors of path lengths between pairs of taxa, have been present in the systematics literature since the early seventies. But, as far as…