Related papers: Toric ideals of homogeneous phylogenetic models

Let $\mathcal{A}=\{{\bf a}_1,\ldots,{\bf a}_n\}\subset\Bbb{N}^m$. We give an algebraic characterization of the universal Markov basis of the toric ideal $I_{\mathcal{A}}$. We show that the Markov complexity of $\mathcal{A}=\{n_1,n_2,n_3\}$…

Phylogenetic networks are a generalization of phylogenetic trees allowing for the representation of non-treelike evolutionary events such as hybridization. Typically, such networks have been analyzed based on their `level', i.e. based on…

Phylogenetic varieties related to equivariant substitution models have been studied largely in the last years. One of the main objectives has been finding a set of generators of the ideal of these varieties, but this has not yet been…

We identify a structural pattern in the construction of known infinite families of trees whose independence polynomials are not log-concave. Using this pattern and properties of polynomial ring ideals, we derive linear recurrences for these…

The space of n (ordered) points on the projective line, modulo automorphisms of the line, is one of the most important and classical examples of an invariant theory quotient, and is one of the first examples given in any course. Generators…

Assuming sufficiently many terms of a n-dimensional table defined over a field are given, we aim at guessing the linear recurrence relations with either constant or polynomial coefficients they satisfy. In many applications, the table terms…

We introduce an infinitesimal Hopf algebra of planar trees, generalising the construction of the non-commutative Connes-Kreimer Hopf algebra. A non-degenerate pairing and a dual basis are defined, and a combinatorial interpretation of the…

Let S be a polynomial algebra over a field. If I is the edge ideal of a perfect semiregular tree, then we give precise formulas for values of depth, Stanley depth, projective dimension, regularity and Krull dimension of S/I.

Inference of species networks from genomic data under the Network Multispecies Coalescent Model is currently severely limited by heavy computational demands. It also remains unclear how complicated networks can be for consistent inference…

Applying a method to reconstruct a phylogenetic tree from random data provides a way to detect whether that method has an inherent bias towards certain tree `shapes'. For maximum parsimony, applied to a sequence of random 2-state data, each…

Let $I \subseteq R = \mathbb{K}[x_1,\ldots,x_n]$ be a toric ideal, i.e., a binomial prime ideal. We investigate when the ideal $I$ can be "split" into the sum of two smaller toric ideals. For a general toric ideal $I$, we give a sufficient…

With a main tool is signed graphs, we give a full description of the characteristic quasi-polynomials of ideals of classical root systems ($ABCD$) with respect to the integer and root lattices. As a result, we obtain a full description of…

To integer programming problems, computational algebraic approaches using Grobner bases or standard pairs via the discreteness of toric ideals have been studied in recent years. Although these approaches have not given improved time…

We investigate projective varieties which are geometric models of binary symmetric phylogenetic 3-valent trees. We prove that these varieties have Gorenstein terminal singularities (with small resolution) and they are Fano varieties of…

We present families of tableaux which interpolate between the classical semi-standard Young tableaux and matching field tableaux. Algebraically, this corresponds to SAGBI bases of Pl\"ucker algebras. We show that each such family of…

We find two bases for the lattices of the SU(2)-TQFT-theory modules of the torus over given rings of integers. We use variant of the bases defined in [GMW]for the lattices of the SO(3)-TQFT-theory modules of the torus. Moreover, we discuss…

The general Markov plus invariable sites (GM+I) model of biological sequence evolution is a two-class model in which an unknown proportion of sites are not allowed to change, while the remainder undergo substitutions according to a Markov…

Equivariant tree models are statistical models used in the reconstruction of phylogenetic trees from genetic data. Here equivariant refers to a symmetry group imposed on the root distribution and on the transition matrices in the model. We…

In this paper we present an algorithm for computing Groebner bases of linear ideals in a difference polynomial ring over a ground difference field. The input difference polynomials generating the ideal are also assumed to be linear. The…

We consider Gibbs distributions on finite random plane trees with bounded branching. We show that as the order of the tree grows to infinity, the distribution of any finite neighborhood of the root of the tree converges to a limit. We…