Related papers: Phylogenetic trees and homomorphisms

We study countable embedding-universal and homomorphism-universal structures and unify results related to both of these notions. We show that many universal and ultrahomogeneous structures allow a concise description (called here a finite…

In mathematical phylogenetics, evolutionary relationships are often represented by trees and networks. The latter are typically used whenever the relationships cannot be adequately described by a tree, which happens when so-called…

Phylogenomics heavily relies on well-curated sequence data sets that consist, for each gene, exclusively of 1:1-orthologous. Paralogs are treated as a dangerous nuisance that has to be detected and removed. We show here that this severe…

A large class of phylogenetic networks can be obtained from trees by the addition of horizontal edges between the tree edges. These networks are called tree based networks. Reticulation-visible networks and child-sibling networks are all…

This thesis investigates the central role of homomorphism problems (structure-preserving maps) in two complementary domains: database querying over finite, graph-shaped data, and constraint solving over (potentially infinite) structures.…

Tangle structure trees, introduced in [3], offer a unified data structure that displays all the tangles of a graph or data set together with certificates for the non-existence of any other tangles, either locally or overall. In this paper…

End-spaces of infinite graphs naturally generalise the Freudenthal boundary and sit at the interface between graph theory, geometric group theory and topology. Our main result is that every end-space can topologically be represented by a…

Lov\'asz (1967) showed that two graphs $G$ and $H$ are isomorphic if and only if they are homomorphism indistinguishable over the class of all graphs, i.e. for every graph $F$, the number of homomorphisms from $F$ to $G$ equals the number…

A family T of digraphs is a complete set of obstructions for a digraph H if for an arbitrary digraph G the existence of a homomorphism from G to H is equivalent to the non-existence of a homomorphism from any member of T to G. A digraph H…

We introduce (weak) oddomorphisms of graphs which are homomorphisms with additional constraints based on parity. These maps turn out to have interesting properties (e.g., they preserve planarity), particularly in relation to homomorphism…

Phylogenetics is the study of the evolutionary relationships between organisms. One of the main challenges in the field is to take biological data for a group of organisms and to infer an evolutionary tree, a graph that represents these…

The Pathwidth Theorem states that if a class of graphs has unbounded pathwidth, then it contains all trees as graph minors. We prove a similar result for dense graphs. More precisely, we give a finite family of tree-like patterns and prove…

Recent years have seen a rapid expansion of the model space explored in statistical phylogenetics, emphasizing the need for new approaches to statistical model representation and software development. Clear communication and representation…

Phylogenetic networks are a generalization of phylogenetic trees to leaf-labeled directed acyclic graphs that represent ancestral relationships between species whose past includes non-tree-like events such as hybridization and horizontal…

We show that all the tangles in a finite graph or matroid can be distinguished by a single tree-decomposition that is invariant under the automorphisms of the graph or matroid. This comes as a corollary of a similar decomposition theorem…

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 hierarchical structure describing the inter-relationships of species has long been a fundamental concept in systematic biology, from Linnean classification through to the more recent quest for a 'Tree of Life.' In this paper we use an…

Rooted phylogenetic networks are used to describe evolutionary histories that contain non-treelike evolutionary events such as hybridization and horizontal gene transfer. In some cases, such histories can be described by a phylogenetic…

There are hierarchical characteristics in the network and how to effectively reveal the hierarchical characteristics in the network is a problem in the research of network structure. If a node is assigned to the community to which it…

Much information about a graph can be obtained by studying its spanning trees. On the other hand, a graph can be regarded as a 1-dimensional cell complex, raising the question of developing a theory of trees in higher dimension. As observed…