Related papers: Reconstruction of caterpillar tanglegrams
A function on an algebra is congruence preserving if, for any congruence, it maps pairs of congruent elements onto pairs of congruent elements. We show that on the algebra of complete binary trees whose leaves are labeled by letters of an…
Peca suggested in a recent paper on the arxiv to consider binary butterfly trees and their Horton-Strahler numbers. The trees are obtained by glueing two binary trees together in a special way; the results are again binary trees but with a…
Increasingly, biologists are constructing evolutionary trees on large numbers of overlapping sets of taxa, and then combining them into a `supertree' that classifies all the taxa. In this paper, we ask how much coverage of the total set of…
A model of the regular arrangement of leaves on a plant stem (phyllotactic patterns) is proposed, based on a new plant pattern algorithm. Tripartite patterning is proposed to occur by the interaction of two signaling pathways. Each pathway…
Binary rooted trees, both in the ordered and in the un-ordered case, are well studied structures in the field of combinatorics. The aim of this work is to study particular patterns in these classes of trees. We consider completely…
It is known that any two trees on the same $n$ leaves can be displayed by a network with $n-2$ reticulations, and there are two trees that cannot be displayed by a network with fewer reticulations. But how many reticulations are needed to…
In this paper, we estimate the weak saturation numbers of trees. As a case study, we examine caterpillars and obtain several tight estimates. In particular, this implies that for any $\alpha\in [1,2]$, there exist caterpillars with $k$…
We consider the phylogenetic tree reconstruction problem with insertions and deletions (indels). Phylogenetic algorithms proceed under a model where sequences evolve down the model tree, and given sequences at the leaves, the problem is to…
A phylogenetic tree shows the evolutionary relationships among species. Internal nodes of the tree represent speciation events and leaf nodes correspond to species. A goal of phylogenetics is to combine such trees into larger trees, called…
A flip in a plane spanning tree $T$ is the operation of removing one edge from $T$ and adding another edge such that the resulting structure is again a plane spanning tree. For trees on a set of points in convex position we study two…
This paper presents a new kind of self-balancing ternary search trie that uses a randomized balancing strategy adapted from Aragon and Seidel's randomized binary search trees ("treaps"). After any sequence of insertions and deletions of…
We elaborate the two-fold simplex-like structures of tree amplitudes in planar maximally supersymmetric Yang-Mills (N=4 SYM), through its connection to a mathematical structure known as the positive Grassmannian. Exploiting the reduced…
A matching complex of a simple graph $G$ is a simplicial complex with faces given by the matchings of $G$. The topology of matching complexes is mysterious; there are few graphs for which the homotopy type is known. Marietti and Testa…
We combine the two fundamental fixed-order tangle theorems of Robertson and Seymour into a single theorem that implies both, in a best possible way. We show that, for every $k \in \mathbb{N}$, every tree-decomposition of a graph $G$ which…
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…
We demonstrate theoretical and experimentally how it is possible to manipulate an entangled angular spectrum of twin beams, in order to reconstruct correlated images with coincidence detection. The entangled angular spectrum comes from the…
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…
Tandem duplication is the process of inserting a copy of a segment of DNA adjacent to the original position. Motivated by applications that store data in living organisms, Jain et al. (2017) proposed the study of codes that correct tandem…
We give closed form expressions for the numbers of multi-rooted plane trees with specified degrees of root vertices. This results in an infinite number of integer sequences some of which are known to have an alternative interpretation. We…
We investigate the number of permutations that occur in random labellings of trees. This is a generalisation of the number of subpermutations occurring in a random permutation. It also generalises some recent results on the number of…