Related papers: Phylogenetic trees and homomorphisms

We study homomorphism polynomials, which are polynomials that enumerate all homomorphisms from a pattern graph $H$ to $n$-vertex graphs. These polynomials have received a lot of attention recently for their crucial role in several new…

We characterise gaps in the full homomorphism order of graphs.

Recent work has proven the existence of extreme inbreeding in a European ancestry sample taken from the contemporary UK population \cite{nature_01}. This result brings our attention again to a math problem related to inbreeding family trees…

In contrast to the abundance of "direct" Ramsey results for classes of finite structures (such as finite ordered graphs, finite ordered metric spaces and finite posets with a linear extension), in only a handful of cases we have a…

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

It has long been known in universal algebra that any distributive sublattice of congruences of an algebra which consists entirely of commuting congruences yields a sheaf representation of the algebra. In this paper we provide a…

Phylogenetic networks are a generalization of phylogenetic trees allowing for the representation of non-treelike evolutionary events such as hybridization. Typically, such networks have been analyzed based on their `level', i.e. based on…

We show how an image can, in principle, be described by the tangles of the graph of its pixels. The tangle-tree theorem provides a nested set of separations that efficiently distinguish all the distinguishable tangles in a graph. This…

The twin-width of a graph measures its distance to co-graphs and generalizes classical width concepts such as tree-width or rank-width. Since its introduction in 2020 (Bonnet et. al. 2020), a mass of new results has appeared relating twin…

Phylogenetic networks are a generalisation of phylogenetic trees that allow for more complex evolutionary histories that include hybridisation-like processes. It is of considerable interest whether a network can be considered `tree-like' or…

Tree alignment graphs (TAGs) provide an intuitive data structure for storing phylogenetic trees that exhibits the relationships of the individual input trees and can potentially account for nested taxonomic relationships. This paper…

This is a survey article on trees, with a modest number of proofs to give a flavor of the way these topologies can be efficiently handled. Trees are defined in set-theorist fashion as partially ordered sets in which the elements below each…

Arboreal networks are a generalization of rooted trees, defined by keeping the tree-like structure, but dropping the requirement for a single root. Just as the class of cographs is precisely the class of undirected graphs that can be…

We extend the closed graph theorem and the open mapping theorem to a context in which a natural duality interchanges their extensions.

Structural information of phylogenetic tree topologies plays an important role in phylogenetic inference. However, finding appropriate topological structures for specific phylogenetic inference tasks often requires significant design effort…

A tanglegram consists of two rooted binary trees and a perfect matching between their leaves, and a planar tanglegram is one that admits a layout with no crossings. We show that the problem of generating planar tanglegrams uniformly at…

While finite graphs have tree-decompositions that efficiently distinguish all their tangles, locally finite graphs with thick ends need not have such tree-decompositions. We show that every locally finite graph without thick ends admits…

Many real life networks present an average path length logarithmic with the number of nodes and a degree distribution which follows a power law. Often these networks have also a modular and self-similar structure and, in some cases -…

A phylogenetic tree shows the evolutionary relationships among species. Internal nodes of the tree represent speciation events and leaf nodes correspond to species. A goal of phylogenetics is to combine such trees into larger trees, called…

Evolutionary models used for describing molecular sequence variation suppose that at a non-recombining genomic segment, sequences share ancestry that can be represented as a genealogy--a rooted, binary, timed tree, with tips corresponding…