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Found 10 papers, 1 papers with code
The weighted total cophenetic index: A novel balance index for phylogenetic networks
For example, for phylogenetic trees, it is common to use balance indices to draw conclusions concerning the underlying evolutionary model, and more than twenty such indices have been proposed and are used for different purposes.
The Theory of Gene Family Histories
Most genes are part of larger families of evolutionary related genes.
Relative Timing Information and Orthology in Evolutionary Scenarios
The relative timing information of gene and species divergences is captured by three colored graphs that have the extant genes as vertices and the species in which the genes are found as vertex colors: the equal-divergence-time (EDT) graph, the later-divergence-time (LDT) graph and the prior-divergence-time (PDT) graph, which together form an edge partition of the complete graph.
Clustering Systems of Phylogenetic Networks
The main results are correspondences of classes of networks and clustering system of the following form: If $N$ is a network of type $\mathbb{X}$, then $\mathcal{C}_N$ satisfies $\mathbb{Y}$, and conversely if $\mathscr{C}$ is a clustering system satisfying $\mathbb{Y}$ then there is network $N$ of type $\mathbb{X}$ such that $\mathscr{C}\subseteq\mathscr{C}_N$. This, in turn, allows us to investigate the mutual dependencies between the distinct types of networks in much detail.
Cayley Graphs of Semigroups Applied to Atom Tracking in Chemistry
While atom tracking with isotope-labeled compounds is an essential and sophisticated wet-lab tool in order to, e. g., illuminate reaction mechanisms, there exists only a limited amount of formal methods to approach the problem.
From Modular Decomposition Trees to Rooted Median Graphs
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 of $\delta$ in labeled trees.
Combinatorics Discrete Mathematics
Arc-Completion of 2-Colored Best Match Graphs to Binary-Explainable Best Match Graphs
For the special case of two-colored BMGs, this leads to a characterization of the least resolved trees (LRTs) of binary-explainable trees and a simple, polynomial-time algorithm for the minimum cardinality completion of the arc set of a BMG to reach a BMG that can be explained by a binary tree.
Data Structures and Algorithms Discrete Mathematics Combinatorics Populations and Evolution
Least resolved trees for two-colored best match graphs
Introducing the concept of support vertices we derive an $O(|V|+|E|\log^2|V|)$-time algorithm to recognize 2-BMGs and to construct its LRT.
Indirect Identification of Horizontal Gene Transfer
An edge in an LDT graph implies that the two corresponding genes are separated by at least one HGT event.
