Related papers: Enumerative combinatorics of unlabeled and labeled…
In this work, we answer an open problem in the study of phylogenetic networks. Phylogenetic trees are rooted binary trees in which all edges are directed away from the root, whereas phylogenetic networks are rooted acyclic digraphs. For the…
Certain families of combinatorial objects admit recursive descriptions in terms of generating trees: each node of the tree corresponds to an object, and the branch leading to the node encodes the choices made in the construction of the…
We consider the problem of uniformly generating a spanning tree, of a connected undirected graph. This process is useful to compute statistics, namely for phylogenetic trees. We describe a Markov chain for producing these trees. For cycle…
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.…
Counting non-isomorphic tree-like multigraphs that include self-loops and multiple edges is an important problem in combinatorial enumeration, with applications in chemical graph theory, polymer science, and network modeling. Traditional…
We present a new definition of non-ambiguous trees (NATs) as labelled binary trees. We thus get a differential equation whose solution can be described combinatorially. This yield a new formula for the number of NATs. We also obtain…
Given a gene tree and a species tree, ancestral configurations represent the combinatorially distinct sets of gene lineages that can reach a given node of the species tree. They have been introduced as a data structure for use in the…
Full binary trees naturally represent commutative non-associative products. There are many important examples of these products: finite-precision floating-point addition and NAND gates, among others. Balance in such a tree is highly…
We study the portraits of isometries of rooted trees - the labelling of the tree, at each vertex, by the permutation of its descendants - in terms of languages. We characterize regularly branched self-similar groups in terms of…
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…
Rooted phylogenetic networks are used to describe evolutionary histories that contain non-treelike evolutionary events such as hybridization and horizontal gene transfer. In some cases, such histories can be described by a phylogenetic…
We consider the NP-hard Tree Containment problem that has important applications in phylogenetics. The problem asks if a given leaf-labeled network contains a subdivision of a given leaf-labeled tree. We develop a fast algorithm for the…
We describe Galois connections which arise between two kinds of combinatorial structures, both of which generalize trees with labelled leaves, and then apply those connections to a family of polytopes. The graphs we study can be imbued with…
Trees are useful entities allowing to model data structures and hierarchical relationships in networked decision systems ubiquitously. An ordered tree is a rooted tree where the order of the subtrees (children) of a node is significant. In…
In this paper, we study a regular rooted coloured tree with random labels assigned to its edges, where the distribution of the label assigned to an edge depends on the colours of its endpoints. We obtain some new results relevant to this…
We obtain a generating function for the degree sequences and colors of rooted multipartite labeled series-reduced trees. As an application of this result, we determine the number of symbolic ultrametrics (introduced by B\"ocker and Dress)…
We present a new definition of non-ambiguous trees (NATs) as labelled binary trees. We thus get a differential equation whose solution can be described combinatorially. This yields a new formula for the number of NATs. We also obtain…
Phylogenetic tree shapes capture fundamental signatures of evolution. We consider ``ranked'' tree shapes, which are equipped with a total order on the internal nodes compatible with the tree graph. Recent work has established an elegant…
Binary trees are fundamental objects in models of evolutionary biology and population genetics. Here, we discuss some of their combinatorial and structural properties as they depend on the tree class considered. Furthermore, the process by…
Merge trees are fundamental structures in topological data analysis. Interleaving distance is a widely accepted metric for comparing merge trees, with applications in visualization and scientific computing. While a greedy algorithm exists…