Related papers: On symmetries in phylogenetic trees

We provide a new geometric representation of a family of fragmentation processes by nested laminations, which are compact subsets of the unit disk made of noncrossing chords. We specifically consider a fragmentation obtained by cutting a…

We introduce a logical foundation to reason on tree structures with constraints on the number of node occurrences. Related formalisms are limited to express occurrence constraints on particular tree regions, as for instance the children of…

Let $\Phi$ be a subset of the simple roots of a (possibly non-reduced) abstract root system $\Sigma$, and let $\lambda \in \Sigma$. We define the $\Phi$-string of $\lambda$ as the set of elements in $\Sigma \cup \{0\}$ of the form $\lambda…

Let $\mathcal{T}_n$ be the set of trees with $n$ vertices. Suppose that each tree in $\mathcal{T}_n$ is equally likely. We show that the number of different rooted trees of a tree equals $(\mu_r+o(1))n$ for almost every tree of…

For an undirected tree with $n$ edges labelled by single letters, we consider its substrings, which are labels of the simple paths between pairs of nodes. We prove that there are $O(n^{1.5})$ different palindromic substrings. This solves an…

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 study a link between complete non-ambiguous trees (CNATs) and permutations exhibited by Daniel Chen and Sebastian Ohlig in recent work. In this, they associate a certain permutation to the leaves of a CNAT, and show that the number of…

The Sackin and Colless indices are two widely-used metrics for measuring the balance of trees and for testing evolutionary models in phylogenetics. This short paper contributes two results about the Sackin and Colless indices of trees. One…

This paper studies the "explanation problem" for tree- and linearly-ordered array data, a problem motivated by database applications and recently solved for the one-dimensional tree-ordered case. In this paper, one is given a matrix A whose…

We present here a new and universal approach for the study of random and/or trees, unifying in one framework many different models, including some novel ones not yet understood in the literature. An and/or tree is a Boolean expression…

The size of the largest common subtree (maximum agreement subtree) of two independent uniform random binary trees on $n$ leaves is known to be between orders $n^{1/8}$ and $n^{1/2}$. By a construction based on recursive splitting and…

We prove that finding a rooted subtree with at least $k$ leaves in a digraph is a fixed parameter tractable problem. A similar result holds for finding rooted spanning trees with many leaves in digraphs from a wide family $\cal L$ that…

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…

Tree balance plays an important role in different research areas like theoretical computer science and mathematical phylogenetics. For example, it has long been known that under the Yule model, a pure birth process, imbalanced trees are…

The reconstruction of phylogenetic networks is an important but challenging problem in phylogenetics and genome evolution, as the space of phylogenetic networks is vast and cannot be sampled well. One approach to the problem is to solve the…

We present a $\lg n + 2 \lg \lg n+3$ ancestry labeling scheme for trees. The problem was first presented by Kannan et al. [STOC 88'] along with a simple $2 \lg n$ solution. Motivated by applications to XML files, the label size was improved…

Phylogenetic trees describe the evolutionary history of a group of present-day species from a common ancestor. These trees are typically reconstructed from aligned DNA sequence data. In this paper we analytically address the following…

In a recent paper, the question of determining the fraction of binary trees that contain a fixed pattern known as the snowflake was posed. We show that this fraction goes to 1, providing two very different proofs: a purely combinatorial one…

Working with generating functions, the combinatorics of a recurrence relation can be expressed in a way that allows for more efficient calculation of the quantity. This is true of the Catalan numbers for an ordered binary tree…

An evolutionary tree (phylogenetic tree) is a binary, rooted, unordered tree that models the evolutionary history of currently living species in which leaves are labeled by species. In this paper, we investigate the problem of finding the…