Related papers: Phylogenetic trees and homomorphisms
We study dualities between classes of relational topological structures, given by Hom-functors. We show that there exists a 2-element structure with infinitely many relations, which reconstructs all other structures generated by a 2-element…
The dominating graph of a graph $H$ has as its vertices all dominating sets of $H$, with an edge between two dominating sets if one can be obtained from the other by the addition or deletion of a single vertex of $H$. In this paper we prove…
We show that every graph admits a canonical tree-like decomposition into its $k$-edge-connected pieces for all $k\in\mathbb{N}\cup\{\infty\}$ simultaneously.
We consider infinite connected quasi-transitive locally finite graphs and show that every such graph with more than one end is a tree amalgamation of two other such graphs. This can be seen as a graph-theoretical version of Stallings'…
The Shannon capacity of graphs, introduced by Shannon in 1956 to model zero-error communication, asks for determining the rate of growth of independent sets in strong powers of graphs. Much is still unknown about this parameter, for…
Fitch graphs $G=(X,E)$ are di-graphs that are explained by $\{\otimes,1\}$-edge-labeled rooted trees with leaf set $X$: there is an arc $xy\in E$ if and only if the unique path in $T$ that connects the least common ancestor…
Phylogenetic trees are widely used to display estimates of how groups of species evolved. Each phylogenetic tree can be seen as a collection of clusters, subgroups of the species that evolved from a common ancestor. When phylogenetic trees…
Directed cographs (di-cographs) play a crucial role in the reconstruction of evolutionary histories of genes based on homology relations which are binary relations between genes. A variety of methods based on pairwise sequence comparisons…
Phylogenetic networks are increasingly used in evolutionary biology to represent the history of species that have undergone reticulate events such as horizontal gene transfer, hybrid speciation and recombination. One of the most fundamental…
The competition graph of a doubly partial order is known to be an interval graph. The CCE graph and the niche graph of a doubly partial order are also known to be interval graphs if the graphs do not contain a cycle of length four and three…
In recent work, the authors developed a simple method of constructing topological spaces from certain well-behaved partially ordered sets -- those coming from sequences of relations between finite sets. This method associates a given poset…
For a connected graph, a path containing all vertices is known as \emph{Hamiltonian path}. For general graphs, there is no known necessary and sufficient condition for the existence of Hamiltonian paths and the complexity of finding a…
Horizontal gene transfer events partition a gene tree $T$ and thus, its leaf set into subsets of genes whose evolutionary history is described by speciation and duplication events alone. Indirect phylogenetic methods can be used to infer…
It is shown that if T is a connected nontrivial graph and X is an arbitrary finite simplicial complex, then there is a graph G such that the complex Hom(T,G) is homotopy equivalent to X. The proof is constructive, and uses a nerve lemma.…
We introduce a general theory of parametrized objects in the setting of infinity categories. Although spaces and spectra parametrized over spaces are the most familiar examples, we establish our theory in the generality of objects of a…
Binary relations derived from labeled rooted trees play an import role in mathematical biology as formal models of evolutionary relationships. The (symmetrized) Fitch relation formalizes xenology as the pairs of genes separated by at least…
Treewidth is a parameter that emerged from the study of minor closed classes of graphs (i.e. classes closed under vertex and edge deletion, and edge contraction). It in some sense describes the global structure of a graph. Roughly, a graph…
Motivated by very large-scale communication networks, we newly introduce exponentiation of graphs. Using the exponential operation on graphs, we can construct various graphs of multi-exponential order with logarithmic diameter. We show that…
We extend Edmonds' Branching Theorem to locally finite infinite digraphs. As examples of Oxley or Aharoni and Thomassen show, this cannot be done using ordinary arborescences, whose underlying graphs are trees. Instead we introduce the…
In biological experiments researchers often have information in the form of a graph that supplements observed numerical data. Incorporating the knowledge contained in these graphs into an analysis of the numerical data is an important and…