Related papers: The Structure of 2-Colored Best Match Graphs
Recent investigations in computational biology focus on a family of 2-colored digraphs, called 2-colored best match graphs, which naturally arise from rooted phylogenetic trees. Actually the defining properties of such graphs are…
Best match graphs (BMGs) are vertex-colored digraphs that naturally arise in mathematical phylogenetics to formalize the notion of evolutionary closest genes w.r.t. an a priori unknown phylogenetic tree. BMGs are explained by unique least…
2-colored quasi best match graphs (2-qBMGs) are directed graphs that arose in phylogenetics. Investigations of 2-qBMGs have mostly focused on computational issues. However, 2-qBMGs also have relevant properties for structural graph theory;…
2-colored best match graphs (2-BMGs) form a subclass of sink-free bi-transitive graphs that appears in phylogenetic combinatorics. There, 2-BMGs describe evolutionarily most closely related genes between a pair of species. They are…
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 mathematical phylogenetics, evolutionary relationships are often represented by trees and networks. The latter are typically used whenever the relationships cannot be adequately described by a tree, which happens when so-called…
An \emph{acyclic coloring} of a graph is a proper vertex coloring such that the union of any two color classes induces a disjoint collection of trees. The more restricted notion of \emph{star coloring} requires that the union of any two…
Reciprocal best matches play an important role in numerous applications in computational biology, in particular as the basis of many widely used tools for orthology assessment. Nevertheless, very little is known about their mathematical…
Quasi-best match graphs (qBMGs) are a hereditary class of directed, properly vertex-colored graphs. They arise naturally in mathematical phylogenetics as a generalization of best match graphs, which formalize the notion of evolutionary…
We consider acyclic r-colorings in graphs and digraphs: they color the vertices in r colors, each of which induces an acyclic graph or digraph. (This includes the dichromatic number of a digraph, and the arboricity of a graph.) For any…
An $acyclic$ edge coloring of a graph is a proper edge coloring such that there are no bichromatic cycle s. The \emph{acyclic chromatic index} of a graph is the minimum number k such that there is an acyclic e dge coloring using k colors…
We consider vertex coloring of an acyclic digraph $\Gdag$ in such a way that two vertices which have a common ancestor in $\Gdag$ receive distinct colors. Such colorings arise in a natural way when bounding space for various genetic data…
It is well-known that an undirected graph has no odd cycle if and only if it is bipartite. A less obvious, but similar result holds for directed graphs: a strongly connected digraph has no odd cycle if and only if it is bipartite. Can this…
Best match graphs (BMG) are a key intermediate in graph-based orthology detection and contain a large amount of information on the gene tree. We provide a near-cubic algorithm to determine whether a BMG is binary-explainable, i.e., whether…
In this paper, we consider a number of results and seven conjectures on properly edge-coloured (PC) paths and cycles in edge-coloured multigraphs. We overview some known results and prove new ones. In particular, we consider a family of…
In this paper we study graphs which admit acyclic orientations that contain a pair of arc-disjoint out-branching and in-branching (such an orientation is called good) and we focus on edge-minimal such graphs. A 2T-graph is a graph whose…
Bipartite graphs have received some attention in the study of social networks and of biological mutualistic systems. A generalization of a previous model is presented, that evolves the topology of the graph in order to optimally account for…
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…
An edge-colouring is {\em strong} if every colour class is an induced matching. In this work we give a formulae that determines either the optimal or the optimal plus one strong chromatic index of bipartite outerplanar graphs. Further, we…
Color-constrained subgraph problems are those where we are given an edge-colored (directed or undirected) graph and the task is to find a specific type of subgraph, like a spanning tree, an arborescence, a single-source shortest path tree,…