Related papers: A bijection between phylogenetic trees and plane o…
A phylogenetic tree is a way to organize a finite set of species, individuals or other sources of related data. The species for which we have existing DNA data make up the set of leaves of the tree. The balanced minimal evolution method of…
An order-theoretic forest is a countable partial order such that the set of elements larger than any element is linearly ordered. It is an order-theoretic tree if any two elements have an upper-bound. The order type of a branch can be any…
We study the enumeration of spinal tree-child phylogenetic networks, a rigid family of tree-child networks in which all internal vertices lie on a single root--to--leaf path. We provide two complementary combinatorial frameworks. First, we…
The history of gene families -- which are equivalent to event-labeled gene trees -- can to some extent be reconstructed from empirically estimated evolutionary event-relations containing pairs of orthologous, paralogous or xenologous genes.…
Phylogenetic networks are used to represent the evolutionary history of species. They are versatile when compared to traditional phylogenetic trees, as they capture more complex evolutionary events such as hybridization and horizontal gene…
In this paper, we shall construct a bijection between rook placements on double staircases (introduced by Josuat-Verg\`es in 2017) and increasing binary trees. We introduce two subclasses of rook placements on double staircases, which we…
Understanding the dynamics of genome rearrangements is a major issue of phylogenetics. Phylogenetics is the study of species evolution. A major goal of the field is to establish evolutionary relationships within groups of species, in order…
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…
Rooted phylogenetic networks provide an explicit representation of the evolutionary history of a set $X$ of sampled species. In contrast to phylogenetic trees which show only speciation events, networks can also accommodate reticulate…
We present a bijection between permutation matrices and descending plane partitions without special parts, which respects the quadruple of statistics considered by Behrend, Di Francesco and Zinn--Justin. This bijection involves 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…
Phylogenetics is a branch of computational biology that studies the evolutionary relationships among biological entities. Its long history and numerous applications notwithstanding, inference of phylogenetic trees from sequence data remains…
Species trees represent the historical divergences of populations or species, while gene trees trace the ancestry of individual gene copies sampled within those populations. In cases involving rapid speciation, gene trees with topologies…
Phylogenetic networks represent evolutionary history of species and can record natural reticulate evolutionary processes such as horizontal gene transfer and gene recombination. This makes phylogenetic networks a more comprehensive…
Tree sets are posets with additional structure that generalize tree-like objects in graphs, matroids, or other combinatorial structures. They are a special class of abstract separation systems. We study infinite tree sets and how they…
Arboreal networks are multi-rooted phylogenetic networks whose underlying graph is a tree. We give an encoding of stack-free arboreal networks in terms of triplets and the novel concept of a duet. This yields a polynomial time algorithm to…
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…
A phylogenetic tree is an edge-weighted binary tree, with leaves labelled by a collection of species, that represents the evolutionary relationships between those species. For such a tree, a phylogenetic diversity index is a function that…
We study varieties that contain unranked tree languages over all alphabets. Trees are labeled with symbols from two alphabets, an unranked operator alphabet and an alphabet used for leaves only. Syntactic algebras of unranked tree languages…
A large class of phylogenetic networks can be obtained from trees by the addition of horizontal edges between the tree edges. These networks are called tree based networks. Reticulation-visible networks and child-sibling networks are all…