Related papers: Restricted generating trees for weak orderings
We consider here the problem of chaining seeds in ordered trees. Seeds are mappings between two trees Q and T and a chain is a subset of non overlapping seeds that is consistent with respect to postfix order and ancestrality. This problem…
Understanding the evolution of a set of genes or species is a fundamental problem in evolutionary biology. The problem we study here takes as input a set of trees describing {possibly discordant} evolutionary scenarios for a given set of…
In this paper we introduce {\em weak ascent sequences}, a class of number sequences that properly contains ascent sequences. We show how these sequences uniquely encode each of the following objects: permutations avoiding a particular…
We introduce and study the model of simply generated non-crossing partitions, which are, roughly speaking, chosen at random according to a sequence of weights. This framework encompasses the particular case of uniform non-crossing…
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…
We discuss a notion of convergence for binary trees that is based on subtree sizes. In analogy to recent developments in the theory of graphs, posets and permutations we investigate some general aspects of the topology, such as a…
A spanning tree of a graph $G$ is a connected acyclic spanning subgraph of $G$. We consider enumeration of spanning trees when $G$ is a $2$-tree, meaning that $G$ is obtained from one edge by iteratively adding a vertex whose neighborhood…
Let $\T_{n}$ be the set of rooted labeled trees on $\set{0,...,n}$. A maximal decreasing subtree of a rooted labeled tree is defined by the maximal subtree from the root with all edges being decreasing. In this paper, we study a new…
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 sample of n generic points in the xy-plane defines a permutation that relates their ranks along the two axes. Every subset of k points similarly defines a pattern, which occurs in that permutation. The number of occurrences of small…
In this paper, we study the problem of constructing a network by observing ordered connectivity constraints, which we define herein. These ordered constraints are made to capture realistic properties of real-world problems that are not…
We describe a generating tree approach to the enumeration and exhaustive generation of k-nonnesting set partitions and permutations. Unlike previous work in the literature using the connections of these objects to Young tableaux and…
We derive tight bounds on the expected weights of several combinatorial optimization problems for random point sets of size $n$ distributed among the leaves of a balanced hierarchically separated tree. We consider {\it monochromatic} and…
Weighted recursive trees are built by adding successively vertices with predetermined weights to a tree: each new vertex is attached to a parent chosen at random with probability proportional to its weight. In the case where the total…
We consider the well-studied pattern counting problem: given a permutation $\pi \in \mathbb{S}_n$ and an integer $k > 1$, count the number of order-isomorphic occurrences of every pattern $\tau \in \mathbb{S}_k$ in $\pi$. Our first result…
Suppose N is a phylogenetic network indicating a complicated relationship among individuals and taxa. Often of interest is a much simpler network, for example, a species tree T, that summarizes the most fundamental relationships. The…
We construct forests that span $\mathbb{Z}^d$, $d\geq2$, that are stationary and directed, and whose trees are infinite, but for which the subtrees attached to each vertex are as short as possible. For $d\geq3$, two independent copies of…
We begin a systematic study of the enumerative combinatorics of mixed succession rules, which are succession rules such that, in the associated generating tree, the nodes are allowed to produce their sons at several different levels…
We consider growing random recursive trees in random environment, in which at each step a new vertex is attached (by an edge of a random length) to an existing tree vertex according to a probability distribution that assigns the tree…
LRM-Trees are an elegant way to partition a sequence of values into sorted consecutive blocks, and to express the relative position of the first element of each block within a previous block. They were used to encode ordinal trees and to…