Related papers: Phylogenetic trees and homomorphisms
\"Uberhomology is a recently defined homology theory for simplicial complexes, which yields subtle information on graphs. We prove that bold homology, a certain specialisation of \"uberhomology, is related to dominating sets in graphs. To…
We relate the existence problem of universal objects to the properties of corresponding enriched categories (lifts or expansions). In particular, extending earlier results, we prove that for every (possibly infinite) regular set F of finite…
Schmidt characterised the class of rayless graphs by an ordinal rank function, which makes it possible to prove statements about rayless graphs by transfinite induction. Halin asked whether Schmidt's rank function can be generalised to…
We define an algebraic setup of homology for hypergraphs, which defaults to simplicial homology in the case of graphs, and study its basic properties. As part of our study we define algebraic spanning trees of hypergraphs, along with…
Deciding whether a graph can be embedded in a grid using only unit-length edges is NP-complete, even when restricted to binary trees. However, it is not difficult to devise a number of graph classes for which the problem is polynomial, even…
In evolutionary biology, phylogenetic networks are graphs that provide a flexible framework for representing complex evolutionary histories that involve reticulate evolutionary events. Recently phylogenetic studies have started to focus on…
We prove that for every $d\geq 3$ the homomorphism order of the class of line graphs of finite graphs with maximal degree $d$ is universal. This means that every finite or countably infinite partially ordered set may be represented by line…
In the homomorphism order of digraphs, a duality pair is an ordered pair of digraphs $(G,H)$ such that for any digraph, $D$, $G\to D$ if and only if $D\not\to H$. The directed path on $k+1$ vertices together with the transitive tournament…
Tree sets are abstract structures that can be used to model various tree-shaped objects in combinatorics. Finite tree sets can be represented by finite graph-theoretical trees. We extend this representation theory to infinite tree sets.…
Dynamic graph theory is a novel, growing area that deals with graphs that change over time and is of great utility in modelling modern wireless, mobile and dynamic environments. As a graph evolves, possibly arbitrarily, it is challenging to…
Phylogenetic networks are used to represent the evolutionary history of species. They are versatile when compared to traditional phylogenetic trees, as they capture more complex evolutionary events such as hybridization and horizontal gene…
Coverings of undirected graphs are used in distributed computing, and unfoldings of directed graphs in semantics of programs. We study these two notions from a graph theoretical point of view so as to highlight their similarities, as they…
Phylogenetic trees and networks are leaf-labelled graphs that are used to describe evolutionary histories of species. The Tree Containment problem asks whether a given phylogenetic tree is embedded in a given phylogenetic network. Given a…
Any function can be constructed using a hierarchy of simpler functions through compositions. Such a hierarchy can be characterized by a binary rooted tree. Each node of this tree is associated with a function which takes as inputs two…
For a zero-relation algebra over a field $\mathcal K$, Crawley-Boevey introduced the concept of a tree module and provided a combinatorial description of a basis for the space of homomorphisms between two tree modules--the basis elements…
Invariants for complicated objects such as those arising in phylogenetics, whether they are invariants as matrices, polynomials, or other mathematical structures, are important tools for distinguishing and working with such objects. In this…
Two graphs are homomorphism indistinguishable over a graph class $\mathcal{F}$, denoted by $G \equiv_{\mathcal{F}} H$, if $\operatorname{hom}(F,G) = \operatorname{hom}(F,H)$ for all $F \in \mathcal{F}$ where $\operatorname{hom}(F,G)$…
We show that the category of graphs has the structure of a 2-category with homotopy as the 2-cells. We then develop an explicit description of homotopies for finite graphs, in terms of what we call `spider moves'. We then create a category…
Phylogenetic networks extend phylogenetic trees to model non-vertical inheritance, by which a lineage inherits material from multiple parents. The computational complexity of estimating phylogenetic networks from genome-wide data with…
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…