Related papers: On symmetries in phylogenetic trees

A caterpillar tree is a connected, acyclic, graph in which all vertices are either a member of a central path, or joined to that central path by a single edge. In other words, caterpillar trees are the class of trees which become path…

In this note we discuss trees similar to the Calkin-Wilf tree, a binary tree that enumerates all positive rational numbers in a simple way. The original construction of Calkin and Wilf is reformulated in a more algebraic language, and an…

In evolutionary biology, biologists often face the problem of constructing a phylogenetic tree on a set $X$ of species from a multiset $\Pi$ of partitions corresponding to various attributes of these species. One approach that is used to…

Rooted binary phylogenetic networks are extensions of rooted binary trees, adding reticulation nodes that are designed to represent evolutionary processes that involve hybridization events. Enumerative combinatorics studies have counted…

The set of all permutations with $n$ symbols is a symmetric group denoted by $S_n$. A transposition tree, $T$, is a spanning tree over its $n$ vertices $V_T=${$1, 2, 3, \ldots n$} where the vertices are the positions of a permutation $\pi$…

In this article we consider several probabilistic processes defining random grapha. One of these processes appeared recently in connection with a factorization problem in the symmetric group. For each of the probabilistic processes, we…

We present a new algorithm to explore or count the numerical semigroups of a given genus which uses the unleaved version of the tree of numerical semigroups. In the unleaved tree there are no leaves rather than the ones at depth equal to…

Let $\Sigma$ be Laurent phenomenon (LP) seed of rank $n$, $\mathcal{A}(\Sigma)$, $\mathcal{U}(\Sigma)$ and $\mathcal{L}(\Sigma)$ be its corresponding Laurent phenomenon algebra, upper bound and lower bound respectively. We prove that each…

While every rooted binary phylogenetic tree is determined by its set of displayed rooted triples, such a result does not hold for an arbitrary rooted binary phylogenetic network. In particular, there exist two non-isomorphic rooted binary…

We derive tractable criteria for the consistency of Bayesian tree reconstruction procedures, which constitute a central class of algorithms for inferring common ancestry among DNA sequence samples in phylogenetics. Our results encompass…

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…

This note presents an encoding and a decoding algorithms for a forest of (labelled) rooted uniform hypertrees and hypercycles in linear time, by using as few as $n - 2$ integers in the range $[1,n]$. It is a simple extension of the…

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…

Phylogenetic networks are often constructed by merging multiple conflicting phylogenetic signals into a directed acyclic graph. It is interesting to explore whether a network constructed in this way induces biologically-relevant…

In binary jumbled pattern matching we wish to preprocess a binary string $S$ in order to answer queries $(i,j)$ which ask for a substring of $S$ that is of size $i$ and has exactly $j$ 1-bits. The problem naturally generalizes to…

Phylogenetic networks generalize phylogenetic trees, and have been introduced in order to describe evolution in the case of transfer of genetic material between coexisting species. There are many classes of phylogenetic networks, which can…

A degree sequence is a sequence ${\bf s}=(N_i,i\geq 0)$ of non-negative integers satisfying $1+\sum_i iN_i=\sum_i N_i<\infty$. We are interested in the uniform distribution $\mathbb{P}_{{\bf s}}$ on rooted plane trees whose degree sequence…

We find surprisingly simple formulas for the limiting probability that the rank of a randomly selected vertex in a randomly selected phylogenetic tree or generalized phylogenetic tree is a given integer.

For a labeled tree on the vertex set $\set{1,2,\ldots,n}$, the local direction of each edge $(i\,j)$ is from $i$ to $j$ if $i<j$. For a rooted tree, there is also a natural global direction of edges towards the root. The number of edges…

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…