Related papers: Tree statistics from Matula numbers
We discuss a notion of shuffle for trees which extends the usual notion of a shuffle for two natural numbers. We give several equivalent descriptions, and prove some algebraic and combinatorial properties. In addition, we characterize…
The reconstruction of a central tendency `species tree' from a large number of conflicting gene trees is a central problem in systematic biology. Moreover, it becomes particularly problematic when taxon coverage is patchy, so that not all…
We are interested in the independence number of large random simply generated trees and related parameters, such as their matching number or the kernel dimension of their adjacency matrix. We express these quantities using a canonical…
The tree-metric theorem provides a necessary and sufficient condition for a dissimilarity matrix to be a tree metric, and has served as the foundation for numerous distance-based reconstruction methods in phylogenetics. Our main result is…
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 rank (also known as protection number or leaf-height) of a vertex in a rooted tree is the minimum distance between the vertex and any of its leaf descendants. We consider the sum of ranks over all vertices (known as the security) in…
We consider compositions of natural numbers when there are different types of each natural number. Several recursions as well as some closed formulas for the number of compositions is derived. We also find its relationships with some known…
We introduce a new model of random tree that grows like a random recursive tree, except at some exceptional "doubling events" when the tree is replaced by two copies of itself attached to a new root. We prove asymptotic results for the size…
In a recent paper on 'Estimating Species Trees from Unrooted Gene Trees' Liu and Yu observe that the distance matrix on the underlying taxon set, which is built up from expected internode distances on gene trees under the multispecies…
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…
Based on the Connes--Kreimer Hopf algebra of rooted trees, the rooted tree maps are defined as linear maps on noncommutative polynomial algebra in two indeterminates. It is known that they induce a large class of linear relations for…
Recursive partitioning is the core of several statistical methods including CART, random forest, and boosted trees. Despite the popularity of tree based methods, to date, there did not exist methods for combining multiple trees into a…
In this paper, we study merge trees induced by a discrete Morse function on a tree. Given a discrete Morse function, we provide a method to constructing an induced merge tree and define a new notion of equivalence of discrete Morse…
We study an abstract notion of tree structure which lies at the common core of various tree-like discrete structures commonly used in combinatorics: trees in graphs, order trees, nested subsets of a set, tree-decompositions of graphs and…
In this first paper, we look at the following question: are the properties of the Fibonacci tree still true if we consider a finitely generated tree by the same rules but rooted at a black node? The direct answer is no, but new properties…
We study the growth of a time-ordered rooted tree by probabilistic attachment of new vertices to leaves. We construct a likelihood function of the leaves based on the connectivity of the tree. We take such connectivity to be induced by the…
For a labelled tree on the vertex set $[n]:=\{1,2,..., n\}$, define the direction of each edge $ij$ to be $i\to j$ if $i<j$. The indegree sequence of $T$ can be considered as a partition $\lambda \vdash n-1$. The enumeration of trees with a…
There are several common ways to encode a tree as a matrix, such as the adjacency matrix, the Laplacian matrix (that is, the infinitesimal generator of the natural random walk), and the matrix of pairwise distances between leaves. Such…
We present here a new conjecture for the nature of the Mersenne prime numbers by connecting it with the Collatz-Kakutani problem. By introducing a natural path length on the basis of the Collatz-Kakutani tree, we conjecture that this path…
Elementary arguments show that a tree or forest is determined (up to isomorphism) by binary matroids defined using the adjacency matrix.