Related papers: Phylogenetic trees and homomorphisms
The goal of this work is to decompose random populations with a genealogy in subfamilies of a given degree of kinship and to obtain a notion of infinitely divisible genealogies. We model the genealogical structure of a population by…
Extending the well-known star-comb lemma for infinite graphs, we characterise the graphs that do not contain an infinite comb or an infinite star, respectively, attached to a given set of vertices. We offer several characterisations: in…
Many methods have been developed for finding the commonalities between different organisms to study their phylogeny. The structure of metabolic networks also reveal valuable insights into metabolic capacity of species as well as into the…
We study the problem of conjunctive query evaluation relative to a class of queries; this problem is formulated here as the relational homomorphism problem relative to a class of structures A, wherein each instance must be a pair of…
We introduce a taxonomy of interaction types and show that graphs are focal hypergraphs: every graph is canonically a focal hypergraph via its closed neighbourhood structure, and every graph dynamical model is a special case of the general…
Most genes are part of larger families of evolutionary related genes. The history of gene families typically involves duplications and losses of genes as well as horizontal transfers into other organisms. The reconstruction of detailed gene…
The notion of homomorphism indistinguishability offers a combinatorial framework for characterizing equivalence relations of graphs, in particular equivalences in counting logics within finite model theory. That is, for certain graph…
In the context of reconstructing phylogenetic networks from a collection of phylogenetic trees, several characterisations and subsequently algorithms have been established to reconstruct a phylogenetic network that collectively embeds all…
Given overlapping subsets of a set of taxa (e.g. species), and posterior distributions on phylogenetic tree topologies for each of these taxon sets, how can we infer a posterior distribution on phylogenetic tree topologies for the entire…
The aim of this article is to provide space level maps between configuration spaces of graphs that are predicted by algebraic manipulations of cellular chains. More explicitly, we consider edge contraction and half-edge deletion, and…
In their study of the giant component in inhomogeneous random graphs, Bollob\'as, Janson, and Riordan introduced a class of branching processes parametrized by a possibly unbounded graphon. We prove that the tree structures underlying two…
In enumerative combinatorics, it is often a goal to enumerate both labeled and unlabeled structures of a given type. The theory of combinatorial species is a novel toolset which provides a rigorous foundation for dealing with the…
We establish relations between the bandwidth and the treewidth of bounded degree graphs G, and relate these parameters to the size of a separator of G as well as the size of an expanding subgraph of G. Our results imply that if one of these…
Trees are partial orders in which every element has a linearly ordered set of predecessors. Here we initiate the exploration of the structural theory of trees with the study of different notions of \emph{branching in trees} and of…
Two genes are xenologs in the sense of Fitch if they are separated by at least one horizontal gene transfer event. Horizonal gene transfer is asymmetric in the sense that the transferred copy is distinguished from the one that remains…
The notion of a duality between two derived functors as well as an extension theorem for derived functors to larger categories in which they need not be defined is introduced. These ideas are then applied to extend and study the coext…
Given a graph or a matroid, a tree of tangles is a tree decomposition that displays the structure of the connectivity: every edge of the decomposition tree induces a separation, that is, a way to divide the graph or matroid into two parts;…
We introduce the concept of morphism of pseudogroups generalizing the \'etal\'e morphisms of Haefliger. With our definition, any continuous foliated map induces a morphism between the corresponding holonomy pseudogroups. The main theorem…
We establish basic facts about the varieties of homogeneous polynomials divisible by powers of linear forms, and explain consequences for geometric complexity theory. This includes quadratic set-theoretic equations, a description of the…
Tangle-tree theorems are an important tool in structural graph theory, and abstract separation systems are a very general setting in which tangle-tree theorems can still be formulated and proven. For infinite abstract separation systems, so…