Related papers: Reconstruction of caterpillar tanglegrams

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…

We prove that one can perfectly pack degenerate graphs into complete or dense $n$-vertex quasirandom graphs, provided that all the degenerate graphs have maximum degree $o(\frac{n}{\log n})$, and in addition $\Omega(n)$ of them have at most…

A graph is called set-sequential if its vertices can be labeled with distinct nonzero vectors in $\mathbb{F}_2^n$ such that when each edge is labeled with the sum$\pmod{2}$ of its vertices, every nonzero vector in $\mathbb{F}_2^n$ is the…

In phylogenetics, a central problem is to infer the evolutionary relationships between a set of species $X$; these relationships are often depicted via a phylogenetic tree -- a tree having its leaves univocally labeled by elements of $X$…

Normal networks are an important class of phylogenetic networks that have compelling mathematical properties which align with intuition about inference from genetic data. While tools enabling widespread use of phylogenetic networks in the…

It is an open question whether there exists a polynomial-time algorithm for computing the rotation distances between pairs of extended ordered binary trees. The problem of computing the rotation distance between an arbitrary pair of trees,…

We consider how to index strings, trees and graphs for jumbled pattern matching when we are asked to return a match if one exists. For example, we show how, given a tree containing two colours, we can build a quadratic-space index with…

It is a classical result that an unrooted tree $T$ having positive real-valued edge lengths and no vertices of degree two can be reconstructed from the induced distance between each pair of leaves. Moreover, if each non-leaf vertex of $T$…

Reconciling gene trees with a species tree is a fundamental problem to understand the evolution of gene families. Many existing approaches reconcile each gene tree independently. However, it is well-known that the evolution of gene families…

We suggest a new non-recursive algorithm for constructing a binary search tree given an array of numbers. The algorithm has $O(N)$ time and $O(1)$ memory complexity if the given array of $N$ numbers is sorted. The resulting tree is of…

In this paper we consider the enumeration of binary trees avoiding non-contiguous binary tree patterns. We begin by computing closed formulas for the number of trees avoiding a single binary tree pattern with 4 or fewer leaves and compare…

Processing sentence constituency trees in binarised form is a common and popular approach in literature. However, constituency trees are non-binary by nature. The binarisation procedure changes deeply the structure, furthering constituents…

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…

Motivated by studies of data retrieval in polymer-based storage systems, we consider the problem of reconstructing a multiset of binary strings that have the same length and the same weight from the compositions of their prefixes and…

The input to the agreement problem is a collection $P = \{T_1, T_2, \dots , T_k\}$ of phylogenetic trees, called input trees, over partially overlapping sets of taxa. The question is whether there exists a tree $T$, called an agreement…

Dendrograms are a way to represent evolutionary relationships between organisms. Nowadays, these are inferred based on the comparison of genes or protein sequences by taking into account their differences and similarities. The genetic…

An important problem in evolutionary biology is to reconstruct the evolutionary history of a set $X$ of species. This history is often represented as a phylogenetic network, that is, a connected graph with leaves labelled by elements in $X$…

An earlier characterization of topologically ordered (lexicographic) path-length sequences of binary trees is reformulated in terms of an integrality condition on a scaled Kraft sum of certain subsequences (full segments, or islands). The…

We demonstrate the versatility of the tangle-tree duality theorem for abstract separation systems by using it to prove tree-of-tangles theorems. This approach allows us to strengthen some of the existing tree-of-tangles theorems by bounding…

In this article, we construct explicit examples of pairs of non-isomorphic trees with the same restricted $U$-polynomial for every $k$; by this we mean that the polynomials agree on terms with degree at most $k+1$. The main tool for this…