Related papers: The Pythagorean Tree: A New Species
We compare three basic kinds of discrete mathematical models used to portray phylogenetic relationships among species and higher taxa: phylogenetic trees, Hennig trees and Nelson cladograms. All three models are trees, as that term is…
Tangle structure trees, introduced in [3], offer a unified data structure that displays all the tangles of a graph or data set together with certificates for the non-existence of any other tangles, either locally or overall. In this paper…
A tree-based network on a set $X$ of $n$ leaves is said to be universal if any rooted binary phylogenetic tree on $X$ can be its base tree. Francis and Steel showed that there is a universal tree-based network on $X$ in the case of $n=3$,…
This paper investigates two involutions on binary trees. One is the mirror symmetry of binary trees which combined with the classical bijection $\varphi$ between binary trees and plane trees answers an open problem posed by Bai and Chen.…
In mathematical phylogenetics, the time-consistent galled trees provide a simple class of rooted binary network structures that can be used to represent a variety of different biological phenomena. We study the enumerative combinatorics of…
Maxmin trees are labeled trees with the property that each vertex is either a local maximum or a local minimum. Such trees were originally introduced by Postnikov, who gave a formula to count them and different combinatorial interpretations…
We investigate the number of permutations that occur in random labellings of trees. This is a generalisation of the number of subpermutations occurring in a random permutation. It also generalises some recent results on the number of…
The problem of enumerating meanders -- pairs of simple plane curves with transverse intersections -- was formulated about forty years ago and is still far from solved. Recently, it was discovered that meanders admit a factorization into…
Following Poupard's study of strictly ordered binary trees with respect to two parameters, namely, "end of minimal chain" and "parent of maximum leaf" a true Tree Calculus is being developed to solve a partial difference equation system and…
Here we present a new fixed parameter tractable algorithm to compute the hybridization number r of two rooted, not necessarily binary phylogenetic trees on taxon set X in time (6^r.r!).poly(n)$, where n=|X|. The novelty of this approach is…
The dual of a map is a fundamental construction on combinatorial maps, but many other combinatorial objects also possess their notion of duality. For instance, the Tamari lattice is isomorphic to its order dual, which induces an involution…
Ever since it was published by Neugebauer and Sachs in 1945, the Old Babylonian tablet known as Plimpton 322 has been the subject of numerous studies leading to different and often conflicting interpretations of it. Overall, the tablet is…
Recently, Han obtained two hook length formulas for binary trees and asked for combinatorial proofs. One of Han's formulas has been generalized to k-ary trees by Yang. Sagan has found a probabilistic proof of Yang's extension. We give…
We consider the phylogenetic tree model in which every node of the tree is observed and binary and the transitions are given by the same matrix on each edge of the tree. We are able to compute the Grobner basis and Markov basis of the toric…
We consider the model of random trees introduced by Devroye [SIAM J. Comput. 28 (1999) 409-432]. The model encompasses many important randomized algorithms and data structures. The pieces of data (items) are stored in a randomized fashion…
In [Dugan-Glennon-Gunnells-Steingrimsson-2019], the authors introduce tiered trees to define combinatorial objects counting absolutely indecomposable representations of certain quivers, and torus orbits on certain homogeneous varieties. In…
We introduce a new family of higher-rank graphs, whose construction was inspired by the graphical techniques of Lambek \cite{Lambek} and Johnstone \cite{Johnstone} used for monoid and category emedding results. We show that they are planar…
Tutte founded the theory of enumeration of planar maps in a series of papers in the 1960s. Rooted non-separable planar maps are in bijection with West-2-stack-sortable permutations, beta(1,0)-trees introduced by Cori, Jacquard and Schaeffer…
Tree-like tableaux are certain fillings of Ferrers diagrams originally introduced by Aval et al., which are in simple bijections with permutation tableaux coming from Postnikov's study of totally nonnegative Grassmanian and alternative…
We introduce a notion of finite sampling consistency for phylogenetic trees and show that the set of finitely sampling consistent and exchangeable distributions on n leaf phylogenetic trees is a polytope. We use this polytope to show that…