Related papers: Non-binary universal tree-based networks
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…
Networks are ubiquitous in biology and computational approaches have been largely investigated for their inference. In particular, supervised machine learning methods can be used to complete a partially known network by integrating various…
Trees fill many extremal roles in graph theory, being minimally connected and serving a critical role in the definition of $n$-good graphs. In this article, we consider the generalization of trees to the setting of $r$-uniform hypergraphs…
Phylogenetic networks are a type of directed acyclic graph that represent how a set $X$ of present-day species are descended from a common ancestor by processes of speciation and reticulate evolution. In the absence of reticulate evolution,…
We consider the counting problem of the number of \textit{leaf-labeled increasing trees}, where internal nodes may have an arbitrary number of descendants. The set of all such trees is a discrete representation of the genealogies obtained…
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…
Invariants for complicated objects such as those arising in phylogenetics, whether they are invariants as matrices, polynomials, or other mathematical structures, are important tools for distinguishing and working with such objects. In this…
By weighted tree we understand such connected tree,that: a) each its vertex and each edge have a positive integer weight; b) the weight of each vertex is equal to the sum of weights of outgoing edges. Each tree has a binary structure --- we…
A uniform attachment tree is a random tree that is generated dynamically. Starting from a fixed "seed" tree, vertices are added sequentially by attaching each vertex to an existing vertex chosen uniformly at random. Upon observing a large…
Construction of phylogenetic trees and networks for extant species from their characters represents one of the key problems in phylogenomics. While solution to this problem is not always uniquely defined and there exist multiple methods for…
We show that there exists an outerplanar graph on $O(n^{c})$ vertices for $c = \log_2(3+\sqrt{10}) \approx 2.623$ that contains every tree on $n$ vertices as a subgraph. This extends a result of Chung and Graham from 1983 who showed that…
Full binary trees naturally represent commutative non-associative products. There are many important examples of these products: finite-precision floating-point addition and NAND gates, among others. Balance in such a tree is highly…
A general quantum network for implementing non-local control-unitary gates, between remote parties at minimal entanglement cost, is shown to be a rooted-tree structure. Starting from a five party scenario, we demonstrate the local…
We introduce the zip tree, a form of randomized binary search tree that integrates previous ideas into one practical, performant, and pleasant-to-implement package. A zip tree is a binary search tree in which each node has a numeric rank…
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…
In this paper we investigate undirected discrete graphical tree models when all the variables in the system are binary, where leaves represent the observable variables and where all the inner nodes are unobserved. A novel approach based on…
Orchards are a biologically relevant class of phylogenetic networks as they can describe treelike evolutionary histories augmented with horizontal transfer events. Moreover, the class has attractive mathematical characterizations that can…
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…
The purpose of this paper is to analyze certain statistics of a recently introduced non-uniform random tree model, biased recursive trees. This model is based on constructing a random tree by establishing a correspondence with non-uniform…
Evolutionary models used for describing molecular sequence variation suppose that at a non-recombining genomic segment, sequences share ancestry that can be represented as a genealogy--a rooted, binary, timed tree, with tips corresponding…