Related papers: Circles and Paths in 2-Colored Best Match Graphs
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…
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…
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…
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…
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…
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…
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…
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 present a foundation study for proper colouring of edge-set graphs. The authors consider that a detailed study of the colouring of edge-set graphs corresponding to the family of paths is best suitable for such foundation…
Path graphs are intersection graphs of paths in a tree. We start from the characterization of path graphs by Monma and Wei [C.L.~Monma,~and~V.K.~Wei, Intersection Graphs of Paths in a Tree, J. Combin. Theory Ser. B, 41:2 (1986) 141--181]…
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…
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…
Drawings of non-planar graphs always result in edge crossings. When there are many edges crossing at small angles, it is often difficult to follow these edges, because of the multiple visual paths resulted from the crossings that slow down…
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…
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…
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,…
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…
Phylogenetic networks are becoming of increasing interest to evolutionary biologists due to their ability to capture complex non-treelike evolutionary processes. From a combinatorial point of view, such networks are certain types of rooted…
One of the most important concepts in biological network analysis is that of network motifs, which are patterns of interconnections that occur in a given network at a frequency higher than expected in a random network. In this work we are…