Related papers: A bijection between phylogenetic trees and plane o…
Using the theory of Properly Embedded Graphs developed in an earlier work we define an involutory duality on the set labeled non-crossing trees that lifts the obvious duality in the set of unlabeled non-crossing trees. The set of…
Phylogenetic trees are a central tool in understanding evolution. They are typically inferred from sequence data, and capture evolutionary relationships through time. It is essential to be able to compare trees from different data sources…
We consider unicellular maps, or polygon gluings, of fixed genus. A few years ago the first author gave a recursive bijection transforming unicellular maps into trees, explaining the presence of Catalan numbers in counting formulas for…
We construct an explicit bijection between bipartite pointed maps of an arbitrary surface $\mathbb{S}$, and specific unicellular blossoming maps of the same surface. Our bijection gives access to the degrees of all the faces, and distances…
By weighted tree we understand such connected tree,that: a) each its vertex and each edge have a positive integer weight; b) the weight of each vertex is equal to the sum of weights of outgoing edges. Each tree has a binary structure --- we…
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…
For a pair consisting of a gene tree and a species tree, the ancestral configurations at an internal node of the species tree are the distinct sets of gene lineages that can be present at that node. Ancestral configurations appear in…
To a given gene tree topology $G$ and species tree topology $S$ with leaves labeled bijectively from a fixed set $X$, one can associate a set of ancestral configurations, each of which encodes a set of gene lineages that can be found at a…
Phylogenomics is a new field which applies to tools in phylogenetics to genome data. Due to a new technology and increasing amount of data, we face new challenges to analyze them over a space of phylogenetic trees. Because a space of…
The in-order traversal provides a natural correspondence between binary trees with a decreasing vertex labeling and endofunctions on a finite set. By suitably restricting the vertex labeling we arrive at a class of trees that we call…
Normal networks are an important class of phylogenetic networks that have compelling mathematical properties which align with intuition about inference from genetic data. While tools enabling widespread use of phylogenetic networks in the…
Elementary arguments show that a tree or forest is determined (up to isomorphism) by binary matroids defined using the adjacency matrix.
A $k$-plane tree is a plane tree whose vertices are assigned labels between $1$ and $k$ in such a way that the sum of the labels along any edge is no greater than $k+1$. These trees are known to be related to $(k+1)$-ary trees, and they are…
As researchers collect increasingly large molecular data sets to reconstruct the Tree of Life, the heterogeneity of signals in the genomes of diverse organisms poses challenges for traditional phylogenetic analysis. A class of phylogenetic…
Phylogenetic network is an evolutionary model that uses a rooted directed acyclic graph (instead of a tree) to model an evolutionary history of species in which reticulate events (e.g., hybrid speciation or horizontal gene transfer)…
Evolutionary histories for species that cross with one another or exchange genetic material can be represented by leaf-labelled, directed graphs called phylogenetic networks. A major challenge in the burgeoning area of phylogenetic networks…
Periodic trees are combinatorial structures which are in bijection with cluster tilting objects in cluster categories of affine type $\tilde{A}_{n-1}$. The internal edges of the tree encode the $c$-vectors corresponding to the cluster…
A bijection is given between multi-edge trees and 3-coloured Motzkin paths.
Construction of phylogenetic trees and networks for extant species from their characters represents one of the key problems in phylogenomics. While solution to this problem is not always uniquely defined and there exist multiple methods for…
In weighted trees, all edges are endowed with positive integral weight. We enumerate weighted bicolored plane trees according to their weight and number of edges.