Related papers: Phylogenetic trees and homomorphisms
We show that every interval in the homomorphism order of finite undirected graphs is either universal or a gap. Together with density and universality this "fractal" property contributes to the spectacular properties of the homomorphism…
We extend to infinite graphs the matroidal characterization of finite graph duality, that two graphs are dual iff they have complementary spanning trees in some common edge set. The naive infinite analogue of this fails. The key in an…
We show the density theorem for the class of finite oriented trees ordered by the homomorphism order. We also show that every interval of oriented trees, in addition to be dense, is in fact universal. We end by considering the fractal…
Homomorphism duality pairs play crucial role in the theory of 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 to be…
We introduce a homotopy theory of digraphs (directed graphs) and prove its basic properties, including the relations to the homology theory of digraphs constructed by the authors in previous papers. In particular, we prove the homotopy…
We prove a general width duality theorem for combinatorial structures with well-defined notions of cohesion and separation. These might be graphs and matroids, but can be much more general or quite different. The theorem asserts a duality…
Phylogenetic networks generalise phylogenetic trees and allow for the accurate representation of the evolutionary history of a set of present-day species whose past includes reticulate events such as hybridisation and lateral gene transfer.…
This work addresses the intrinsic relationship between trees and networks (i.e. graphs). A complete (invertible) mapping is presented which allows trees to be mapped into weighted graphs and then backmapped into the original tree without…
In this paper, we study the graph classification problem from the graph homomorphism perspective. We consider the homomorphisms from $F$ to $G$, where $G$ is a graph of interest (e.g. molecules or social networks) and $F$ belongs to some…
A digraph is connected-homogeneous if any isomorphism between finite connected induced subdigraphs extends to an automorphism of the digraph. We consider locally-finite connected-homogeneous digraphs with more than one end. In the case that…
Rare events have played an increasing role in molecular phylogenetics as potentially homoplasy-poor characters.In this contribution we analyze the phylogenetic information content from a combinatorial point of view by consid-ering the…
A partial order is universal if it contains every countable partial order as a suborder. In 2017, Fiala, Hubi\v{c}ka, Long and Ne\v{s}et\v{r}il showed that every interval in the homomorphism order of graphs is universal, with the only…
We consider constrained variants of graph homomorphisms such as embeddings, monomorphisms, full homomorphisms, surjective homomorpshims, and locally constrained homomorphisms. We also introduce a new variation on this theme which derives…
Phylogenetic trees and networks are leaf-labelled graphs used to model evolution. Display graphs are created by identifying common leaf labels in two or more phylogenetic trees or networks. The treewidth of such graphs is bounded as a…
We apply a recent duality theorem for tangles in abstract separation systems to derive tangle-type duality theorems for width-parameters in graphs and matroids. We further derive a duality theorem for the existence of clusters in large data…
In this series, we introduce and investigate the concept of connectoids, which captures the connectivity structure of various discrete objects such as undirected graphs, directed graphs, bidirected graphs, hypergraphs and finitary matroids.…
We extend the notion of graph homomorphism to cellularly embedded graphs (maps) by designing operations on vertices and edges that respect the surface topology; we thus obtain the first definition of map homomorphism that preserves both the…
Phylogenetic tree shapes capture fundamental signatures of evolution. We consider ``ranked'' tree shapes, which are equipped with a total order on the internal nodes compatible with the tree graph. Recent work has established an elegant…
Phylogenetic networks are a generalization of phylogenetic trees that are used to represent non-tree-like evolutionary histories that arise in organisms such as plants and bacteria, or uncertainty in evolutionary histories. An…
We introduce a comprehensive data structure, tangle structure trees, which simultaneously displays all the $\mathcal{F}$-tangles of an abstract separation system for very general obstruction sets $\mathcal{F}$. It simultaneously also…