Related papers: Phylogenetic trees and homomorphisms

Let $G$ be a complete graph with $n+1$ vertices. In a recent paper of the authors, it is shown that the path trees of the graph play a special role in the structure of the truncated powers and partition functions that are associated with…

We endow the category of bialgebras over a pair of operads in distribution with a cofibrantly generated model category structure. We work in the category of chain complexes over a field of characteristic zero. We split our construction in…

In Graph Minors III, Robertson and Seymour write: "It seems that the tree-width of a planar graph and the tree-width of its geometric dual are approximately equal - indeed, we have convinced ourselves that they differ by at most one". They…

The (A,D) duality pairs play crucial role in the theory of general relational structures and in the Constraint Satisfaction Problem. The case where both classes are finite is fully characterized. The case when both side are infinite seems…

Every generic linear functional $f$ on a convex polytope $P$ induces an orientation on the graph of $P$. From the resulting directed graph one can define a notion of $f$-arborescence and $f$-monotone path on $P$, as well as a natural graph…

Attempting to recognize a tree inside a phylogenetic network is a fundamental undertaking in evolutionary analysis. In the last few years, therefore, tree-based phylogenetic networks, which are defined by a spanning tree called a…

Consider a plane graph G, drawn with straight lines. For every pair a,b of vertices of G, we compare the shortest-path distance between a and b in G (with Euclidean edge lengths) to their actual distance in the plane. The worst-case ratio…

We demonstrate that graph-based models are fully capable of representing higher-order interactions, and have a long history of being used for precisely this purpose. This stands in contrast to a common claim in the recent literature on…

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…

Fitch graphs $G=(X,E)$ are digraphs that are explained by $\{\emptyset, 1\}$-edge-labeled rooted trees $T$ with leaf set $X$: there is an arc $(x,y) \in E$ if and only if the unique path in $T$ that connects the last common ancestor…

Graphs are fundamental data structures which concisely capture the relational structure in many important real-world domains, such as knowledge graphs, physical and social interactions, language, and chemistry. Here we introduce a powerful…

In a series of three papers we develop an end space theory for digraphs. Here in the third paper we introduce a concept of depth-first search trees in infinite digraphs, which we call normal spanning arborescences. We show that normal…

A normal network is uniquely determined by the set of phylogenetic trees that it displays. Given a set $\mathcal{P}$ of rooted binary phylogenetic trees, this paper presents a polynomial-time algorithm that reconstructs the unique binary…

We work out the theory of fractional isomorphism of graphons as a generalization to the classical theory of fractional isomorphism of finite graphs. The generalization is given in terms of homomorphism densities of finite trees and it is…

We study deterministic constructions of graphs for which the unique completion of low rank matrices is generically possible regardless of the values of the entries. We relate the completability to the presence of some patterns (particular…

Phylogenetic trees in genetics and biology in general are all binary. We make an attempt to answer one fundamental question: Is such binary branching from the coarsest to the finest scales sustained by data? We convert this question into an…

Lorea [11] and later Frank et al. [8] generalized graphic matroids to hypergraphic matroids. In [8], the authors introduced hypertrees as a generalization of spanning trees and proved a form of the theorem of Tutte [18] and Nash-Williams…

We prove that every oriented tree on $n$ vertices with bounded maximum degree appears as a spanning subdigraph of every directed graph on $n$ vertices with minimum semidegree at least $n/2+o(n)$. This can be seen as a directed graph…

Increasingly, biologists are constructing evolutionary trees on large numbers of overlapping sets of taxa, and then combining them into a `supertree' that classifies all the taxa. In this paper, we ask how much coverage of the total set of…

Graph invariants provide a powerful analytical tool for investigation of abstract structures of graphs. They, combined in convenient relations, carry global and general information about a graph and its various substructures such as cycle…