Related papers: Quasi-Best Match Graphs
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;…
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…
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…
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…
Best match graphs (BMGs) are vertex-colored directed graphs that were introduced to model the relationships of genes (vertices) from different species (colors) given an underlying evolutionary tree that is assumed to be unknown. In…
2-quasi best match graphs (2-qBMGs) are directed graphs that capture a notion of close relatedness in phylogenetics. Here, we investigate the undirected underlying graph of a 2-qBMG (un-2qBMG) and show that they contain neither a path $P_l$…
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…
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…
Best match graphs (BMGs) are a class of colored digraphs that naturally appear in mathematical phylogenetics and can be approximated with the help of similarity measures between gene sequences, albeit not without errors. The corresponding…
Reciprocal best match graphs (RBMGs) are vertex colored graphs whose vertices represent genes and the colors the species where the genes reside. Edges identify pairs of genes that are most closely related with respect to an underlying…
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…
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…
Recent investigations in computational biology have focused 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…
A wide variety of problems in computational biology, most notably the assessment of orthology, are solved with the help of reciprocal best matches. Using an evolutionary definition of best matches that captures the intuition behind the…
The undirected underlying graph of a 2-quasi best match graph (2-qBMG) is proven not to contain any induced graph isomorphic to $P_6$ or $C_6$. This new feature allows for the investigation of 2-BMGs further by exploiting the numerous known…
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…
For a simple graph G = (V, E), a coloring of vertices of G using two colors, say red and blue, is called a quasi neighborhood balanced coloring if, for every vertex of the graph, the number of red neighbors and the number of blue neighbors…
In the Properly Colored Spanning Tree problem, we are given an edge-colored undirected graph and the goal is to find a properly colored spanning tree, i.e., a spanning tree in which any two adjacent edges have distinct colors. The problem…
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…
A fibration of graphs is an homomorphism that is a local isomorphism of in-neighbourhoods, much in the same way a covering projection is a local isomorphism of neighbourhoods. Recently, it has been shown that graph fibrations are useful…