Related papers: A Short Note on Undirected Fitch Graphs
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,…
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…
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 $(x,y)$…
Assume that there is a free group action of automorphisms on a bipartite graph. If there is a perfect matching on the factor graph, then obviously there is a perfect matching on the graph. Surprisingly, the reversed is also true for…
In evolutionary biology, phylogenetic networks are graphs that provide a flexible framework for representing complex evolutionary histories that involve reticulate evolutionary events. Recently phylogenetic studies have started to focus on…
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…
We generalize the tree-confluent graphs to a broader class of graphs called Delta-confluent graphs. This class of graphs and distance-hereditary graphs, a well-known class of graphs, coincide. Some results about the visualization of…
Bipartite best match graphs (BMG) and their generalizations arise in mathematical phylogenetics as combinatorial models describing evolutionary relationships among related genes in a pair of species. In this work, we characterize the class…
It has recently been shown that, contrary to the wide belief that a shift-enabled condition (necessary for any shift-invariant filter to be representable by a graph shift matrix) can be ignored because any non-shift-enabled matrix can be…
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…
In this note we give a combinatorial characterization of all the unmixed bipartite graphs.
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…
Phylogenetic networks are used to represent the evolutionary history of species. They are versatile when compared to traditional phylogenetic trees, as they capture more complex evolutionary events such as hybridization and horizontal gene…
In Chapter 1 we fully characterise pairs of finite graphs which form a gap in the full homomorphism order. This leads to a simple proof of the existence of generalised duality pairs. We also discuss how such results can be carried to…
The semidirect product of a finitely generated group dual with the symmetric group can be described through so-called group-theoretical categories of partitions (covers only a special case; due to Raum--Weber, 2015) and skew categories of…
We show that if the two parts of a finite bipartite graph have the same degree sequence, then there is a bipartite graph, with the same degree sequences, which is symmetric, in that it has an involutive graph automorphism that interchanges…
A split graph is a graph whose vertices can be partitioned into a clique and a stable set. We investigate the combinatorial species of split graphs, providing species-theoretic generalizations of enumerative results due to B\'ina and…
In this paper, we extend the definition of cohomology associated to monotone graph properties, to encompass twisted functor coefficients. We introduce oriented matchings on graphs, and focus on their (twisted) cohomology groups. We…