Related papers: Arboreal Ultrametrics
Phylogenomics is a new field which applies to tools in phylogenetics to genome data. Due to a new technology and increasing amount of data, we face new challenges to analyze them over a space of phylogenetic trees. Because a space of…
The minimal number of rooted subtree prune and regraft (rSPR) operations needed to transform one phylogenetic tree into another one induces a metric on phylogenetic trees - the rSPR-distance. The rSPR-distance between two phylogenetic trees…
The necessary and sufficient conditions under which a given family $\mathcal{F}$ of subsets of finite set $X$ coincides with the family $\mathbf{B}_X$ of all balls generated by some ultrametric $d$ on $X$ are found. It is shown that the…
Merge trees, a type of topological descriptor, serve to identify and summarize the topological characteristics associated with scalar fields. They present a great potential for the analysis and visualization of time-varying data. First,…
Phylogenetic networks generalize phylogenetic trees, and have been introduced in order to describe evolution in the case of transfer of genetic material between coexisting species. There are many classes of phylogenetic networks, which can…
There are several interrelated notions of discrete curvature on graphs. Many approaches utilize the optimal transportation metric on its probability simplex or the distance matrix of the graph. In this survey article, we compute formulas…
The Robinson-Foulds (RF) metric is arguably the most widely used measure of phylogenetic tree similarity, despite its well-known shortcomings: For example, moving a single taxon in a tree can result in a tree that has maximum distance to…
Phylogenetic trees are leaf-labelled trees used to model the evolution of species. Here we explore the practical impact of kernelization (i.e. data reduction) on the NP-hard problem of computing the TBR distance between two unrooted binary…
The presence of reticulate evolutionary events in phylogenies turn phylogenetic trees into phylogenetic networks. These events imply in particular that there may exist multiple evolutionary paths from a non-extant species to an extant one,…
In this paper we investigate the geometric properties of quasi-trees, and prove some equivalent criteria. We give a general construction of a tree that approximates the ends of a geodesic space, and use this to prove that every quasi-tree…
We investigate the interrelations between the metric properties, order properties and combinatorial properties of the set of balls in totally bounded ultrametric space. In particular, the Gurvich-Vyalyi representation of finite, ultrametric…
Let $T$ be a tree of arbitrary finite or infinite order and let $U(T)$ be the set of all ultrametric spaces generated by vertex labelings of $T$. Let ${\bf US}$ denote the class of all ultrametric spaces generated by vertex labelings of…
A fundamental problem in network science is the normalization of the topological or physical distance between vertices, that requires understanding the range of variation of the unnormalized distances. Here we investigate the limits of the…
Deciding whether there is a single tree -a supertree- that summarizes the evolutionary information in a collection of unrooted trees is a fundamental problem in phylogenetics. We consider two versions of this question: agreement and…
A set of general allometric scaling laws is derived for different systems represented by tree networks. The formulation postulates self-similar networks with an arbitrary number of branches developed in each generation, and with an…
The rank (also known as protection number or leaf-height) of a vertex in a rooted tree is the minimum distance between the vertex and any of its leaf descendants. We consider the sum of ranks over all vertices (known as the security) in…
Recently, so-called treebased phylogenetic networks have gained considerable interest in the literature, where a treebased network is a network that can be constructed from a phylogenetic tree, called the base tree, by adding additional…
Phylogenetic trees represent certain species and their likely ancestors. In such a tree, present-day species are leaves and an edge from u to v indicates that u is an ancestor of v. Weights on these edges indicate the phylogenetic distance.…
Let $S$ be a normal complex analytic surface singularity. We say that $S$ is arborescent if the dual graph of any resolution of it is a tree. Whenever $A,B$ are distinct branches on $S$, we denote by $A \cdot B$ their intersection number in…
It is shown that the rooted trees $T_X$ and $T_Y$ representing finite ultrametric spaces $X$ and $Y$ are isomorphic if and only if there exists a ball-preserving bijection $F:X\to Y$.