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Rooted phylogenetic networks are often constructed by combining trees, clusters, triplets or characters into a single network that in some well-defined sense simultaneously represents them all. We review these four models and investigate…
Banderier, Marchal, and Wallner considered Young tableaux with walls, which are similar to standard Young tableaux, except that local decreases are allowed at some walls. In this work, we prove a conjecture of Fuchs and Yu concerning the…
Rooted phylogenetic networks allow biologists to represent evolutionary relationships between present-day species by revealing ancestral speciation and hybridization events. A convenient and well-studied class of such networks are…
Phylogenetic networks are mathematical structures for modeling and visualization of reticulation processes in the study of evolution. Galled networks, reticulation visible networks, nearly-stable networks and stable-child networks are the…
In recent decades, phylogenetic networks have become a standard tool in modeling evolutionary processes. Nevertheless, basic combinatorial questions about them are still largely open. For instance, even the asymptotic counting problem for…
In previous work, we gave asymptotic counting results for the number of tree-child and normal networks with $k$ reticulation vertices and explicit exponential generating functions of the counting sequences for $k=1,2,3$. The purpose of this…
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…
Phylogenetic networks are a type of leaf-labelled, acyclic, directed graph used by biologists to represent the evolutionary history of species whose past includes reticulation events. A phylogenetic network is tree-child if each non-leaf…
Rooted binary phylogenetic networks are extensions of rooted binary trees, adding reticulation nodes that are designed to represent evolutionary processes that involve hybridization events. Enumerative combinatorics studies have counted…
Phylogenetic trees and networks are graphs used to model evolutionary relationships, with trees representing strictly branching histories and networks allowing for events in which lineages merge, called reticulation events. While the…
This paper introduces a new combinatorial framework for modeling the growth of binary trees through a discrete evolution process that incorporates a growing rule and an extinction rule. Building upon the theory of increasingly labeled…
In this work we introduce and study various generalizations of the notion of increasingly labelled trees, where the label of a child node is always larger than the label of its parent node, to multilabelled tree families, where the nodes in…
Neural Networks and Decision Trees: two popular techniques for supervised learning that are seemingly disconnected in their formulation and optimization method, have recently been combined in a single construct. The connection pivots on…
In phylogenetics, phylogenetic trees are rooted binary trees, whereas phylogenetic networks are rooted arbitrary acyclic digraphs. Edges are directed away from the root and leaves are uniquely labeled with taxa in phylogenetic networks. For…
We provide precise asymptotic estimates for the number of general phylogenetic networks by using analytic combinatorial methods. Recently, this approach is studied by Fuchs, Gittenberger, and the author himself (Australasian Journal of…
In this article, we consider a generalization of Young tableaux in which we allow some consecutive pairs of cells with decreasing labels. We show that this leads to a rich variety of combinatorial formulas, which suggest that these new…
It was recently shown that a large class of phylogenetic networks, the `labellable' networks, is in bijection with the set of `expanding' covers of finite sets. In this paper, we show how several prominent classes of phylogenetic networks…
Phylogenetic networks generalize phylogenetic trees, and have been introduced in order to describe evolution in the case of transfer of genetic material between coexisting species. There are many classes of phylogenetic networks, which can…
We consider a distributed detection system with communication constraints, where several nodes are arranged in an arbitrary tree topology, under the assumption of conditionally independent observations. We propose a cyclic design procedure…
One strategy for reconstruction of phylogenetic networks is to solve the phylogenetic network problem, which involves inferring phylogenetic trees first and subsequently computing the smallest phylogenetic network that displays all the…