Related papers: Phylogenetic trees and homomorphisms
The displayed tree phylogenetic network model is shown to sit as a natural submodel of the graphical model associated to a directed acyclic graph (DAG). This representation allows to derive a number of results about the displayed tree…
Binary trees are fundamental objects in models of evolutionary biology and population genetics. Here, we discuss some of their combinatorial and structural properties as they depend on the tree class considered. Furthermore, the process by…
In this paper, we use the theory of Riordan matrices to introduce the notion of a Riordan graph. The Riordan graphs are a far-reaching generalization of the well known and well studied Pascal graphs and Toeplitz graphs, and also some other…
Phylogenetic networks provide a more general description of evolutionary relationships than rooted phylogenetic trees. One way to produce a phylogenetic network is to randomly place $k$ arcs between the edges of a rooted binary phylogenetic…
In this series we introduce and investigate the concept of connectoids, which captures the connectivity structure of various discrete objects like undirected graphs, directed graphs, bidirected graphs, hypergraphs or finitary matroids. In…
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 -…
We extend the notion of 'homomorphism-homogeneity' to a wider class of kinds of maps than previously studied, and we investigate the relations between the resulting notions of homomorphism-homogeneity, giving several examples. We also give…
We develop a purely set-theoretic formalism for binary trees and binary graphs. We define a category of binary automata, and display it as a fibred category over the category of binary graphs. We also relate the notion of binary graphs to…
We extend the concept of a Hubbard tree, well established and useful in the theory of polynomial dynamics, to the dynamics of transcendental entire functions. We show that Hubbard trees in the strict traditional sense, as invariant compact…
The aim of this chapter is to provide an adequate graph theoretic framework for the description of periodic bifurcations which have recently been discovered in descendant trees of finite p-groups. The graph theoretic concepts of rooted…
In this paper, we revisit the split decomposition of graphs and give new combinatorial and algorithmic results for the class of totally decomposable graphs, also known as the distance hereditary graphs, and for two non-trivial subclasses,…
Horizontal gene transfer is an important contributor to evolution. According to Walter M.\ Fitch, two genes are xenologs if they are separated by at least one HGT. More formally, the directed Fitch graph has a set of genes is its vertices,…
Bilinear maps and their classifying tensor products are well-known in the theory of linear algebra, and their generalization to algebras of commutative monads is a classical result of monad theory. Motivated by constructions needed in…
Phylogenetic networks are becoming of increasing interest to evolutionary biologists due to their ability to capture complex non-treelike evolutionary processes. From a combinatorial point of view, such networks are certain types of rooted…
We consider hereditary classes of graphs equipped with a total order. We provide multiple equivalent characterisations of those classes which have bounded twin-width. In particular, we prove a grid theorem for classes of ordered graphs…
Pairs of graded graphs, together with the Fomin property of graded graph duality, are rich combinatorial structures providing among other a framework for enumeration. The prototypical example is the one of the Young graded graph of integer…
The evolutionary relationships among organisms have traditionally been represented using rooted phylogenetic trees. However, due to reticulate processes such as hybridization or lateral gene transfer, evolution cannot always be adequately…
We study harmonic morphisms of graphs as a natural discrete analogue of holomorphic maps between Riemann surfaces. We formulate a graph-theoretic analogue of the classical Riemann-Hurwitz formula, study the functorial maps on Jacobians and…
Deciding whether a collection of unrooted trees is compatible is a fundamental problem in phylogenetics. Two different graph-theoretic characterizations of tree compatibility have recently been proposed. In one of these, tree compatibility…
We characterize the compatibility of a collection of unrooted phylogenetic trees as a question of determining whether a graph derived from these trees --- the display graph --- has a specific kind of triangulation, which we call legal. Our…