Related papers: A bijection for the evolution of $B$-trees
The Neighbor-Joining algorithm is a popular distance-based phylogenetic method that computes a tree metric from a dissimilarity map arising from biological data. Realizing dissimilarity maps as points in Euclidean space, the algorithm…
Many innovations are inspired by past ideas in a non-trivial way. Tracing these origins and identifying scientific branches is crucial for research inspirations. In this paper, we use citation relations to identify the descendant chart,…
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…
We present a bijective algorithm with which an arbitrary permutation decomposes canonically into elementary blocks which we call families, which are sets with a specified number of ascents and descents. We show that families, arranged in an…
We study the number of distance queries needed to identify certain properties of a hidden tree $T$ on $n$ vertices. A distance query consists of two vertices $x,y$, and the answer is the distance of $x$ and $y$ in $T$. We determine the…
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…
A metric phylogenetic tree relating a collection of taxa induces weighted rooted triples and weighted quartets for all subsets of three and four taxa, respectively. New intertaxon distances are defined that can be calculated from these…
Given two binary trees on $N$ labeled leaves, the quartet distance between the trees is the number of disagreeing quartets. By permuting the leaves at random, the expected quartets distance between the two trees is…
Seo and Shin showed that the number of rooted trees on $[n+1]$ such that the maximal decreasing subtree with the same root has $k+1$ vertices is equal to the number of functions $f:[n]\to[n]$ such that the image of $f$ contains $[k]$. We…
We study a circular order on labelled, m-edge-coloured trees with k vertices, and show that the set of such trees with a fixed circular order is in bijection with the set of RNA m-diagrams of degree k, combinatorial objects which can be…
The widely used model for evolutionary relationships is a bifurcating tree with all taxa/observations placed at the leaves. This is not appropriate if the taxa have been densely sampled across evolutionary time and may be in a direct…
In \cite{BaDeFePi96} the concept of nondecreasing Dyck paths was introduced. We continue this research by looking at it from the point of view of words, rational languages, planted plane trees, and continued fractions. We construct a…
A classical result, fundamental to evolutionary biology, states that an edge-weighted tree $T$ with leaf set $X$, positive edge weights, and no vertices of degree 2 can be uniquely reconstructed from the set of leaf-to-leaf distances…
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…
Phylogenetic networks generalise phylogenetic trees and allow for the accurate representation of the evolutionary history of a set of present-day species whose past includes reticulate events such as hybridisation and lateral gene transfer.…
The purpose of this paper is to analyze certain statistics of a recently introduced non-uniform random tree model, biased recursive trees. This model is based on constructing a random tree by establishing a correspondence with non-uniform…
The mutational heterogeneity of tumours can be described with a tree representing the evolutionary history of the tumour. With noisy sequencing data there may be uncertainty in the inferred tree structure, while we may also wish to study…
Given two messages - as linear sequences of letters, it is immediate to determine whether one can be transformed into the other by simple substitution cipher of the letters. On the other hand, if the letters are carried as labels on nodes…
We construct a direct natural bijection between descending plane partitions without any special part and permutations. The directness is in the sense that the bijection avoids any reference to nonintersecting lattice paths. The advantage of…
We unify and extend previous bijections on plane quadrangulations to bipartite and quasibipartite plane maps. Starting from a bipartite plane map with a distinguished edge and two distinguished corners (in the same face or in two different…