Related papers: Toric ideals of homogeneous phylogenetic models
Statistical models of evolution are algebraic varieties in the space of joint probability distributions on the leaf colorations of a phylogenetic tree. The phylogenetic invariants of a model are the polynomials which vanish on the variety.…
We address the problem of studying the toric ideals of phylogenetic invariants for a general group-based model on an arbitrary claw tree. We focus on the group $\mathbb Z_2$ and choose a natural recursive approach that extends to other…
In this article we consider the problem of finding generators of the toric ideal associated to a combinatorial object called a staged tree. Our main theorem states that toric ideals of staged trees that are balanced and stratified are…
Characteristic imsets are 0-1 vectors which correspond to Markov equivalence classes of directed acyclic graphs. The study of their convex hull, named the characteristic imset polytope, has led to new and interesting geometric perspectives…
Each linear code can be described by a code ideal given as the sum of a toric ideal and a non-prime ideal. In this way, several concepts from the theory of toric ideals can be translated into the setting of code ideals. It will be shown…
The general Markov model of the evolution of biological sequences along a tree leads to a parameterization of an algebraic variety. Understanding this variety and the polynomials, called phylogenetic invariants, which vanish on it, is a…
We introduce and study the toric fiber product of two ideals in polynomial rings that are homogeneous with respect to the same multigrading. Under the assumption that the set of degrees of the variables form a linearly independent set, we…
We introduce equivariant tree models in algebraic statistics, which unify and generalise existing tree models such as the general Markov model, the strand symmetric model, and group based models. We focus on the ideals of such models. We…
Two correspondences have been provided that associate any linear code over a finite field with a binomial ideal. In this paper, algorithms for computing their Graver bases and universal Gr\"obner bases are given. To this end, a connection…
In this paper, we study a class of toric ideals obtained by using some geometric data of ADE trees which are the minimal resolution graphs of rational surface singularities. We compute explicit Gr\"obner bases for these toric ideals that…
We give a combinatorial description of the toric ideal of invariants of the Cavender-Farris-Neyman model with a molecular clock (CFN-MC) on a rooted binary phylogenetic tree and prove results about the polytope associated to this toric…
Every normal toric ideal of codimension two is minimally generated by a Grobner basis with squarefree initial monomials. A polynomial time algorithm is presented for checking whether a toric ideal of fixed codimension is normal.
The universal Gr\"{o}bner basis of $I$, is a Gr\"{o}bner basis for $I$ with respect to all term orders simultaneously. Let $I_G$ be the toric ideal of a graph $G$. We characterize in graph theoretical terms the elements of the universal…
In 1980, White conjectured that the toric ideal of a matroid is generated by quadratic binomials corresponding to a symmetric exchange. In this paper, we compute Gr\"obner bases of toric ideals associated with matroids and show that, for…
The universal Gr\"obner basis of an ideal is a Gr\"obner basis with respect to all term orders simultaneously. The aim of this paper is to present an algorithmic approach to compute the universal Gr\"obner basis for the toric ideal…
We define phylogenetic projective toric model of a trivalent graph as a generalization of a binary symmetric model of a trivalent phylogenetic tree. Generators of the pro- jective coordinate ring of the models of graphs with one cycle are…
We consider the Graver basis, the universal Groebner basis, a Markov basis and the set of the circuits of a toric ideal. Let $A, B$ be any two of these bases such that $A\not \subset B$, we prove that there is no polynomial on the size or…
We find all smooth toric bases that support elliptically fibered Calabi-Yau threefolds, using the intersection structure of the irreducible effective divisors on the base. These bases can be used for F-theory constructions of…
In combinatorial commutative algebra and algebraic statistics many toric ideals are constructed from graphs. Keeping the categorical structure of graphs in mind we give previous results a more functorial context and generalize them by…
In this paper, we discuss the normality of the toric rings of stable set polytopes, and the set of generators and Gr\"obner bases of toric ideals of stable set polytopes by using the results on that of edge polytopes of finite nonsimple…