Related papers: Fitch Graph Completion
Gene conversion is a mechanism by which a double-strand break in a DNA molecule is repaired using a homologous DNA molecule as a template. As a result, one gene is 'copied and pasted' onto the other gene. It was recently reported that the…
Phylogenetic networks generalise phylogenetic trees and allow for the accurate representation of the evolutionary history of a set of present-day species whose past includes reticulate events such as hybridisation and lateral gene transfer.…
In this article, we introduce a relation including ideals of an evolution algebra and hereditary subsets of vertices of its associated graph and establish some properties among them. This relation allows us to determine maximal ideals and…
Phylogenetics is the study of the evolutionary relationships between organisms. One of the main challenges in the field is to take biological data for a group of organisms and to infer an evolutionary tree, a graph that represents these…
Let $\mathcal G$ be a hypergraph whose edges are colored. An {\it $(\alpha,n)$-detachment} of $\mathcal G$ is a hypergraph obtained by splitting a vertex $\alpha$ into $n$ vertices, say $\alpha_1,\dots,\alpha_n$, and sharing the incident…
The genome of bacterial species is much more flexible than that of eukaryotes. Moreover, the distributed genome hypothesis for bacteria states that the total number of genes present in a bacterial population is greater than the genome of…
In a graph, the switching operation reverses adjacencies between a subset of vertices and the others. For a hereditary graph class $\mathcal{G}$, we are concerned with the maximum subclass and the minimum superclass of $\mathcal{G}$ that…
Hybrid evolution and horizontal gene transfer (HGT) are processes where evolutionary relationships may more accurately be described by a reticulated network than by a tree. In such a network, there will often be several paths between any…
The topological structure of complex networks has fascinated researchers for several decades, resulting in the discovery of many universal properties and reoccurring characteristics of different kinds of networks. However, much less is…
The topological structure of complex networks has fascinated researchers for several decades, resulting in the discovery of many universal properties and reoccurring characteristics of different kinds of networks. However, much less is…
Recent years have witnessed the emerging success of graph neural networks (GNNs) for modeling structured data. However, most GNNs are designed for homogeneous graphs, in which all nodes and edges belong to the same types, making them…
A spanning subgraph $F$ of a graph $G$ is called {\em perfect} if $F$ is a forest, the degree $d_F(x)$ of each vertex $x$ in $F$ is odd, and each tree of $F$ is an induced subgraph of $G$. Alex Scott (Graphs \& Combin., 2001) proved that…
In this paper, a new information theoretic framework for graph matching is introduced. Using this framework, the graph isomorphism and seeded graph matching problems are studied. The maximum degree algorithm for graph isomorphism is…
Phylogenetic networks represent evolutionary history of species and can record natural reticulate evolutionary processes such as horizontal gene transfer and gene recombination. This makes phylogenetic networks a more comprehensive…
Treewidth is a parameter that emerged from the study of minor closed classes of graphs (i.e. classes closed under vertex and edge deletion, and edge contraction). It in some sense describes the global structure of a graph. Roughly, a graph…
A family of graphs $\mathcal{F}$ is hereditary if $\mathcal{F}$ is closed under isomorphism and taking induced subgraphs. The speed of $\mathcal{F}$ is the sequence $\{|\mathcal{F}^n|\}_{n \in \mathbb{N}}$, where $\mathcal{F}^n$ denotes the…
Crossover is the process of recombining the genetic features of two parents. For many applications where crossover is applied to permutations, relevant genetic features are pairs of adjacent elements, also called edges in the permutation…
Let $\mathcal{G}_{\alpha}$ be a hereditary graph class (i.e, every subgraph of $G_{\alpha}\in \mathcal{G}_{\alpha}$ belongs to $\mathcal{G}_{\alpha}$) such that every graph $G_{\alpha}$ in $\mathcal{G}_{\alpha}$ has minimum degree at most…
Phylogenetic tree shapes capture fundamental signatures of evolution. We consider ``ranked'' tree shapes, which are equipped with a total order on the internal nodes compatible with the tree graph. Recent work has established an elegant…
Can the vertices of a graph $G$ be partitioned into $A \cup B$, so that $G[A]$ is a line-graph and $G[B]$ is a forest? Can $G$ be partitioned into a planar graph and a perfect graph? The NP-completeness of these problems are just special…