Related papers: Non-binary universal tree-based networks
In this work, we answer an open problem in the study of phylogenetic networks. Phylogenetic trees are rooted binary trees in which all edges are directed away from the root, whereas phylogenetic networks are rooted acyclic digraphs. For the…
Ultametrics are an important class of distances used in applications such as phylogenetics, clustering and classification theory. Ultrametrics are essentially distances that can be represented by an edge-weighted rooted tree so that all of…
Phylogenetic networks are leaf-labelled directed acyclic graphs that are used to describe non-treelike evolutionary histories and are thus a generalization of phylogenetic trees. The hybridization number of a phylogenetic network is the sum…
An order-theoretic forest is a countable partial order such that the set of elements larger than any element is linearly ordered. It is an order-theoretic tree if any two elements have an upper-bound. The order type of a branch can be any…
There exist several methods dealing with the reconstruction of rooted phylogenetic networks explaining different evolutionary histories given by rooted binary phylogenetic trees. In practice, however, due to insufficient information of the…
The comprehensive characterization of the structure of complex networks is essential to understand the dynamical processes which guide their evolution. The discovery of the scale-free distribution and the small world property of real…
The Pathwidth Theorem states that if a class of graphs has unbounded pathwidth, then it contains all trees as graph minors. We prove a similar result for dense graphs. More precisely, we give a finite family of tree-like patterns and prove…
In phylogenetics, evolution is traditionally represented in a tree-like manner. However, phylogenetic networks can be more appropriate for representing evolutionary events such as hybridization, horizontal gene transfer, and others. In…
Phylogenetic trees and networks are leaf-labelled graphs that are used to describe evolutionary histories of species. The Tree Containment problem asks whether a given phylogenetic tree is embedded in a given phylogenetic network. Given a…
The Calkin-Wilf tree is an infinite binary tree whose vertices are the positive rational numbers. Each number occurs in the tree exactly once and in the form $a/b$, where are $a$ and $b$ are relatively prime positive integers. For every…
Galled trees are studied as a recombination model in theoretic population genetics. This class of phylogenetic networks has been generalized to tree-child networks, normal networks and tree-based networks by relaxing a structural condition.…
Given overlapping subsets of a set of taxa (e.g. species), and posterior distributions on phylogenetic tree topologies for each of these taxon sets, how can we infer a posterior distribution on phylogenetic tree topologies for the entire…
The ongoing explosion of genome sequence data is transforming how we reconstruct and understand the histories of biological systems. Across biological scales, from individual cells to populations and species, trees-based models provide a…
This paper considers the enumeration of ternary trees (i.e. rooted ordered trees in which each vertex has 0 or 3 children) avoiding a contiguous ternary tree pattern. We begin by finding recurrence relations for several simple tree…
Quasi-trees generalize trees in that the unique "path" between two nodes may be infinite and have any countable order type. They are used to define the rank-width of a countable graph in such a way that it is equal to the least upper-bound…
One of the important features of an interconnection network is its ability to efficiently simulate programs or parallel algorithms written for other architectures. Such a simulation problem can be mathematically formulated as a graph…
Daily internet communication relies heavily on tree-structured graphs, embodied by popular data formats such as XML and JSON. However, many recent generative (probabilistic) models utilize neural networks to learn a probability distribution…
Inference of species networks from genomic data under the Network Multispecies Coalescent Model is currently severely limited by heavy computational demands. It also remains unclear how complicated networks can be for consistent inference…
Consider a rooted binary tree with n nodes. Assign with the root the abscissa 0, and with the left (resp. right) child of a node of abscissa i the abscissa i-1 (resp. i+1). We prove that the number of binary trees of size n having exactly…
We study the influence of the seed in random trees grown according to the uniform attachment model, also known as uniform random recursive trees. We show that different seeds lead to different distributions of limiting trees from a total…