Related papers: Generalized Fitch Graphs: Edge-labeled Graphs that…
Fitch graphs $G=(X,E)$ are digraphs that are explained by $\{\emptyset, 1\}$-edge-labeled rooted trees $T$ with leaf set $X$: there is an arc $(x,y) \in E$ if and only if the unique path in $T$ that connects the last common ancestor…
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…
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…
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,…
According to Walter M. Fitch, two genes are xenologs if they are separated by at least one horizontal gene transfer. This concept is formalized through Fitch relations, which are defined as binary relations that comprise all pairs $(x,y)$…
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…
Phylogenetic networks generalise phylogenetic trees and allow for the accurate representation of the evolutionary history of a set of present-day species whose past includes reticulate events such as hybridisation and lateral gene transfer.…
A rooted tree $T$ with vertex labels $t(v)$ and set-valued edge labels $\lambda(e)$ defines maps $\delta$ and $\varepsilon$ on the pairs of leaves of $T$ by setting $\delta(x,y)=q$ if the last common ancestor $\text{lca}(x,y)$ of $x$ and…
The modular decomposition of a symmetric map $\delta\colon X\times X \to \Upsilon$ (or, equivalently, a set of symmetric binary relations, a 2-structure, or an edge-colored undirected graph) is a natural construction to capture key features…
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 a type of directed acyclic graph that represent how a set $X$ of present-day species are descended from a common ancestor by processes of speciation and reticulate evolution. In the absence of reticulate evolution,…
Phylogenetic networks are a generalization of phylogenetic trees that are used to represent non-tree-like evolutionary histories that arise in organisms such as plants and bacteria, or uncertainty in evolutionary histories. An…
THIS IS A CORRECTED VERSION INCLUDING AN APPENDED CORRIGENDUM. Best match graphs arise naturally as the first processing intermediate in algorithms for orthology detection. Let $T$ be a phylogenetic (gene) tree $T$ and $\sigma$ an…
In this paper, matching pairs of stocahstically generated graphs in the presence of generalized seed side-information is considered. The graph matching problem emerges naturally in various applications such as social network…
Let $\ell \geqslant 0$ be an integer, and $G$ be a graph without loops. An $\ell$-link of $G$ is a walk of length $\ell$ in which consecutive edges are different. We identify an $\ell$-link with its reverse sequence. The $\ell$-link graph…
To a given gene tree topology $G$ and species tree topology $S$ with leaves labeled bijectively from a fixed set $X$, one can associate a set of ancestral configurations, each of which encodes a set of gene lineages that can be found at a…
The symmetric version of Fitch's xenology relation coincides with class of complete multipartite graph and thus cannot convey any non-trivial phylogenetic information.
Phylogenetic tree shapes capture fundamental signatures of evolution. We consider ``ranked'' tree shapes, which are equipped with a total order on the internal nodes compatible with the tree graph. Recent work has established an elegant…
These notes concern aspects of various graphs whose vertex set is a group $G$ and whose edges reflect group structure in some way (so that they are invariant under the action of the automorphism group of $G$). The graphs I will discuss are…
A geophylogeny is a phylogenetic tree (or dendrogram) where each leaf (e.g. biological taxon) has an associated geographic location (site). To clearly visualize a geophylogeny, the tree is typically represented as a crossing-free drawing…