Related papers: The space of equidistant phylogenetic cactuses
Rooted phylogenetic networks provide a more complete representation of the ancestral relationship between species than phylogenetic trees when reticulate evolutionary processes are at play. One way to reconstruct a phylogenetic network is…
Metric embeddings are central to metric theory and its applications. Here we consider embeddings of a different sort: maps from a set to subsets of a metric space so that distances between points are approximated by minimal distances…
For a growing number of applications such as cellular, peer-to-peer, and sensor networks, efficient error-free transmission of data through a network is essential. Toward this end, K\"{o}tter and Kschischang propose the use of subspace…
Rapid developments in genetics and biology have led to phylogenetic methods becoming an important direction in the study of cancer and viral evolution. Although our understanding of gene biology and biochemistry has increased and is…
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…
Phylogenetic networks are a flexible model of evolution that can represent reticulate evolution and handle complex data. Tree-based networks, which are phylogenetic networks that have a spanning tree with the same root and leaf-set as the…
It is shown that a minimum weight spanning tree of a finite ultrametric space can be always found in the form of path. As a canonical representing tree such path uniquely defines the whole space and, moreover, it has much more simple…
Phylogenetic trees are used to model evolution: leaves are labelled to represent contemporary species ("taxa") and interior vertices represent extinct ancestors. Informally, convex characters are measurements on the contemporary species in…
There are many metrics available to compare phylogenetic trees since this is a fundamental task in computational biology. In this paper, we focus on one such metric, the $\ell^\infty$-cophenetic metric introduced by Cardona et al. This…
Dinits, Karzanov and Lomonosov showed that the minimal edge cuts of a finite graph have the structure of a cactus, a tree-like graph constructed from cycles. Evangelidou and Papasoglu extended this to minimal cuts separating the ends of an…
Pairwise ordered tree alignment are combinatorial objects that appear in RNA secondary structure comparison. However, the usual representation of tree alignments as supertrees is ambiguous, i.e. two distinct supertrees may induce identical…
Let $T$ be a finitely branching rooted tree such that any node has at least two successors. The path space $[T]$ is an ultrametric space: for distinct paths $f,g$ let $d(f,g)= 1/|T_n|$, where $T_n$ denotes the $n$-th level of the tree, and…
The reconstruction of phylogenetic trees from molecular sequence data relies on modelling site substitutions by a Markov process, or a mixture of such processes. In general, allowing mixed processes can result in different tree topologies…
We present a framework for embedding graph structured data into a vector space, taking into account node features and topology of a graph into the optimal transport (OT) problem. Then we propose a novel distance between two graphs, named…
We give a de Finetti type representation for exchangeable random coalescent trees (formally described as semi-ultrametrics) in terms of sampling iid sequences from marked metric measure spaces. We apply this representation to define…
An important problem in phylogenetics is the construction of phylogenetic trees. One way to approach this problem, known as the supertree method, involves inferring a phylogenetic tree with leaves consisting of a set $X$ of species from a…
It is well known that the Tits boundary of a proper cocompact CAT(0) space embeds into every asymptotic cone of the space. We explore the relationships between the asymptotic cones of a CAT(0) space and its boundary under both the standard…
We develop a unified spectral framework for finite ultrametric phylogenetic trees, grounding the analysis of phylogenetic structure in operator theory and stochastic dynamics in the finite setting. For a given finite ultrametric measure…
Compatibility of unrooted phylogenetic trees is a well studied problem in phylogenetics. It asks to determine whether for a set of k input trees there exists a larger tree (called a supertree) that contains the topologies of all k input…
We investigate path-, ray- and branch spaces of trees, certain topological spaces naturally associated with order theoretic trees, and provide topological characterisations for these spaces in terms of the existence of certain kinds of…