Related papers: Phylogenetic degrees for Jukes-Cantor model

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…

Results of Koebe (1936), Schramm (1992), and Springborn (2005) yield realizations of $3$-polytopes with edges tangent to the unit sphere. Here we study the algebraic degrees of such realizations. This initiates the research on constrained…

Let k be an algebraically closed field. Given an extension A : B of finite-dimensional k- algebras, we establish criteria ensuring that the representation-theoretic notion of polynomial growth is preserved under ascent and descent. These…

We consider the counting problem of the number of \textit{leaf-labeled increasing trees}, where internal nodes may have an arbitrary number of descendants. The set of all such trees is a discrete representation of the genealogies obtained…

The grand challenges in biology today are being shaped by powerful high-throughput technologies that have revealed the genomes of many organisms, global expression patterns of genes and detailed information about variation within…

We give an explicit upper bound for the degree of a tropical basis of a homogeneous polynomial ideal. As an application f-vectors of tropical varieties are discussed. Various examples illustrate differences between Gr\"obner and tropical…

A hypertoric variety is a quaternionic analogue of a toric variety. Just as the topology of toric varieties is closely related to the combinatorics of polytopes, the topology of hypertoric varieties interacts richly with the combinatorics…

Phylogenetic networks generalize phylogenetic trees by allowing the modelization of events of reticulate evolution. Among the different kinds of phylogenetic networks that have been proposed in the literature, the subclass of binary…

Phylogenetic diversity is a measure for describing how much of an evolutionary tree is spanned by a subset of species. If one applies this to the (unknown) subset of current species that will still be present at some future time, then this…

Phylogenetic networks represent evolutionary histories of sets of taxa where horizontal evolution or hybridization has occurred. Placing a Markov model of evolution on a phylogenetic network gives a model that is particularly amenable to…

Distances between sequences based on their $k$-mer frequency counts can be used to reconstruct phylogenies without first computing a sequence alignment. Past work has shown that effective use of k-mer methods depends on 1) model-based…

Bayesian phylogenetics is vital for understanding evolutionary dynamics, and requires accurate and efficient approximation of posterior distributions over trees. In this work, we develop a variational Bayesian approach for ultrametric…

A (convex) polytope $P$ is said to be $2$-level if for every direction of hyperplanes which is facet-defining for $P$, the vertices of $P$ can be covered with two hyperplanes of that direction. The study of these polytopes is motivated by…

We investigate Gauss maps of (not necessarily normal) projective toric varieties over an algebraically closed field of arbitrary characteristic. The main results are as follows: (1) The structure of the Gauss map of a toric variety is…

We prove an explicit degree formula for certain unitary Deligne-Lusztig varieties. Combining with an alternative degree formula in terms of Schubert calculus, we deduce several algebraic combinatorial identities which may be of independent…

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…

Phylogenetic trees are binary nonplanar trees with labelled leaves, and plane oriented recursive trees are planar trees with an increasing labelling. Both families are enumerated by double factorials. A bijection is constructed, using the…

The theory of algebras with polynomial identities has developed significantly, with special attention devoted to the classification of varieties according to the asymptotic behavior of their codimension sequences. This sequence is a…

We develop a probabilistic algorithm for computing elimination ideals of likelihood equations, which is for larger models by far more efficient than directly computing Groebner bases or the interpolation method proposed in the first…

In different areas of discrete mathematics, a certain type of polynomials, having coefficients in a field K of finite characteristic, has been considered. The form and the degree of these polynomials, here called projective, are simply…