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A mixed graph can be seen as a type of digraph containing some edges (two opposite arcs). Here we introduce the concept of sequence mixed graphs, which is a generalization of both sequence graphs and iterated line digraphs. These structures…

Evolutionary scenarios describing the evolution of a family of genes within a collection of species comprise the mapping of the vertices of a gene tree $T$ to vertices and edges of a species tree $S$. The relative timing of the last common…

A biased graph consists of a graph $G$ together with a collection of distinguished cycles of $G$, called balanced cycles, with the property that no theta subgraph contains exactly two balanced cycles. Perhaps the most natural biased graphs…

Phylogenetic networks and, more generally, directed acyclic graphs (DAGs) represent hierarchical structure beyond trees, for instance in the presence of reticulate evolutionary events such as hybridization or horizontal gene transfer. A…

We present a concept called the branch-depth of a connectivity function, that generalizes the tree-depth of graphs. Then we prove two theorems showing that this concept aligns closely with the notions of tree-depth and shrub-depth of graphs…

We define joint exchangeability on arrays indexed by a vector of natural numbers with coordinates being the vertices of directed acyclic graphs (DAGs) using local isomorphisms. The notion provides a new version of exchangeability, which is…

Since Darwin, species trees have been used as a simplified description of the relationships which summarize the complicated network $N$ of reality. Recent evidence of hybridization and lateral gene transfer, however, suggest that there are…

We give a precise description of combed trees in terms of Kelly-Mac Lane graphs. We show that any combed tree is uniquely expressed as an allowable Kelly-Mac Lane graph of a certain shape. Conversely, we show that any such Kelly-Mac Lane…

In phylogenetics, tree-based networks are used to model and visualize the evolutionary history of species where reticulate events such as horizontal gene transfer have occurred. Formally, a tree-based network $N$ consists of a phylogenetic…

The modular decomposition of a graph $G$ is a natural construction to capture key features of $G$ in terms of a labeled tree $(T,t)$ whose vertices are labeled as "series" ($1$), "parallel" ($0$) or "prime". However, full information of $G$…

Exact pattern matching in labeled graphs is the problem of searching paths of a graph $G=(V,E)$ that spell the same string as the pattern $P[1..m]$. This basic problem can be found at the heart of more complex operations on variation graphs…

We show that the directed labelled Cayley graphs coincide with the rooted deterministic vertex-transitive simple graphs. The Cayley graphs are also the strongly connected deterministic simple graphs of which all vertices have the same cycle…

For a spanning tree T of a connected graph G and for a labelling \phi: E(T) \rightarrow {+, -}, \phi is called an alternating sign on a spanning tree T of a graph G if for any cotree edge e \in E(G)-E(T), the unique path in T joining both…

A connected and nonempty graph A is defined as generalized t-edge distance-balanced, while for each edge f={\alpha}\{beta} the number of edges nearer to {\alpha} than \{beta} are equal to t-times of edges nearer to \{beta} than to {\alpha},…

Rooted phylogenetic networks, or more generally, directed acyclic graphs (DAGs), are widely used to model species or gene relationships that traditional rooted trees cannot fully capture, especially in the presence of reticulate processes…

In this paper, we study the graph classification problem from the graph homomorphism perspective. We consider the homomorphisms from $F$ to $G$, where $G$ is a graph of interest (e.g. molecules or social networks) and $F$ belongs to some…

For a graph $G = (V, E)$, the $\gamma$-graph of $G$, denoted $G(\gamma) = (V(\gamma), E(\gamma))$, is the graph whose vertex set is the collection of minimum dominating sets, or $\gamma$-sets of $G$, and two $\gamma$-sets are adjacent in…

Given a graph $G=(V,E)$, an integer $k$, and a function $f_G:V^k \times V^k \to {0,1}$, the $k^{th}$ graph product of $G$ w.r.t $f_G$ is the graph with vertex set $V^k$, and an edge between two vertices $x=(x_1,...,x_k)$ and…

In 1968, Erd\"os defined the Shift Graph as the graph whose vertices are the $k$-element subsets of $[n]=\{0,1,2,...,n-1\}$ such that $A=\{a_1,...,a_k\}$ and $B=\{b_1,...,b_k\}$ are neighbours iff $a_1<b_1=a_2<b_2=a_3<... <b_{n-1}=a_n<b_n$.…

Phylogenetic networks are rooted acyclic directed graphs in which the leaves are identified with members of a set X of species. The cluster of a vertex is the set of leaves that are descendants of the vertex. A network is "distinct-cluster"…