Related papers: The space of equidistant phylogenetic cactuses
We define and give explicit construction of the universal tree-graded space with a given collection of pieces. We apply that to proving uniqueness of asymptotic cones of relatively hyperbolic groups whose peripheral subgroups have unique…
Phylogenetic networks are a special type of graph which generalize phylogenetic trees and that are used to model non-treelike evolutionary processes such as recombination and hybridization. In this paper, we consider {\em unrooted}…
Phylogenetic networks are rooted acyclic directed graphs in which the leaves are identified with members of a set X of species. The cluster of a vertex is the set of leaves that are descendants of the vertex. A network is "distinct-cluster"…
Associated to any finite metric space are a large number of objects and quantities which provide some degree of structural or geometric information about the space. In this paper we show that in the setting of subsets of weighted Hamming…
We introduce two new tools for studying CAT(0) spaces: \emph{curtains}, versions of cubical hyperplanes; and the \emph{curtain model}, a counterpart of the curve graph. These tools shed new light on CAT(0) spaces, allowing us to prove a…
We introduce the notion of metric semilattice on the metric space and prove the criterion of $\R$-tree as connected geodesic metric space $X$ admitting the partial order, such that $X$ is semilinear metric semilattice. Also we state the…
The evolutionary relationships among organisms have traditionally been represented using rooted phylogenetic trees. However, due to reticulate processes such as hybridization or lateral gene transfer, evolution cannot always be adequately…
The $r$-th cactus variety of a subvariety $X$ in a projective space generalizes the $r$-th secant variety of $X$ and it is defined using linear spans of finite subschemes of $X$ of degree $r$. One of its original purposes was to study the…
We study the evolution of branching trees embedded in Euclidean spaces with suppressed branching of spatially close nodes. This cooperative branching process accounts for the effect of overcrowding of nodes in the embedding space and mimics…
Ultrametric trees are trees whose leaves lie at the same distance from the root. They are used to model the genealogy of a population of particles co-existing at the same point in time. We show how the boundary of an ultrametric tree, like…
We call a \emph{comb} a map $f:I\to [0,\infty)$, where $I$ is a compact interval, such that $\{f\ge \varepsilon\}$ is finite for any $\varepsilon$. A comb induces a (pseudo)-distance $\dtf$ on $\{f=0\}$ defined by $\dtf(s,t) =…
Phylogenetic networks are a type of leaf-labelled, acyclic, directed graph used by biologists to represent the evolutionary history of species whose past includes reticulation events. A phylogenetic network is tree-child if each non-leaf…
In Francis and Steel (2015), it was shown that there exists non-trivial networks on $4$ leaves upon which the distance metric affords a metric on a tree which is not the base tree of the network. In this paper we extend this result in two…
Phylogenetic networks generalize phylogenetic trees in order to model reticulation events. Although the comparison of phylogenetic trees is well studied, and there are multiple ways to do it in an efficient way, the situation is much…
Phylogenetic trees summarize evolutionary relationships. The Billera-Holmes-Vogtmann (BHV) space for comparing phylogenetic trees has many elegant mathematical properties, but it does not encompass trees with differing leaf sets. To…
In this article we study the treewidth of the \emph{display graph}, an auxiliary graph structure obtained from the fusion of phylogenetic (i.e., evolutionary) trees at their leaves. Earlier work has shown that the treewidth of the display…
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…
It was recently observed by de Vienne et al. that a simple square root transformation of distances between taxa on a phylogenetic tree allowed for an embedding of the taxa into Euclidean space. While the justification for this was based on…
This paper introduces decorated merge trees (DMTs) as a novel invariant for persistent spaces. DMTs combine both $\pi_0$ and $H_n$ information into a single data structure that distinguishes filtrations that merge trees and persistent…
Let $X$ be a proper, geodesically complete CAT(0) space which satisfies Chen and Eberlein's duality condition. We show the existence of a strong notion of rank for $X$ by proving that the parallel sets $P_v$ of geodesics $v$ in $X$ are…