Related papers: Toric ideals of homogeneous phylogenetic models

We introduce the package PhylogeneticTrees for Macaulay2 which allows users to compute phylogenetic invariants for group-based tree models. We provide some background information on phylogenetic algebraic geometry and show how the package…

We call an ideal in a polynomial ring robust if it can be minimally generated by a universal Gr\"obner basis. In this paper we show that robust toric ideals generated by quadrics are essentially determinantal. We then discuss two possible…

We study the combinatorics of Gr\"obner degenerations of Grassmannians and the Schubert varieties inside them. We provide a family of binomial ideals whose combinatorics is governed by tableaux induced by matching fields in the sense of…

Given a parametric polynomial ideal I, the algorithm DISPGB, introduced by the author in 2002, builds up a binary tree describing a dichotomic discussion of the different reduced Groebner bases depending on the values of the parameters,…

Extending the notion of indispensable binomials of a toric ideal, we define indispensable monomials of a toric ideal and establish some of their properties. They are useful for searching indispensable binomials of a toric ideal and for…

In $1980$ White conjectured that every element of the toric ideal of a matroid is generated by quadratic binomials corresponding to symmetric exchanges. We prove White's conjecture for high degrees with respect to the rank. This extends our…

The edges of any hypergraph parametrize a monomial algebra called the edge subring of the hypergraph. We study presentation ideals of these edge subrings, and describe their generators in terms of balanced walks on hypergraphs. Our results…

Motivated by the construction of Newton--Okounkov bodies and toric degenerations via cluster algebras in [GHKK18, FO25], we consider a family of Newton--Okounkov polytopes of a complex smooth Fano variety $X$ related by a composition of…

We describe the universal Groebner basis of the ideal of maximal minors and the ideal of $2$-minors of a multigraded matrix of linear forms. Our results imply that the ideals are radical and provide bounds on the regularity. In particular,…

Let $G$ be a finite connected simple graph and $I_{G}$ the toric ideal of the edge ring $K[G]$ of $G$. In the present paper, we study finite graphs $G$ with the property that $I_{G}$ is generated by quadratic binomials and $I_{G}$ possesses…

Phylogenetic networks are a generalisation of phylogenetic trees that allow for more complex evolutionary histories that include hybridisation-like processes. It is of considerable interest whether a network can be considered `tree-like' or…

We define a new balance index for rooted phylogenetic trees based on the symmetry of the evolutive history of every set of 4 leaves. This index makes sense for multifurcating trees and it can be computed in time linear in the number of…

Topological phylogenetic trees can be assigned edge weights in several natural ways, highlighting different aspects of the tree. Here the rooted triple and quartet metrizations are introduced, and applied to formulate novel fast methods of…

We introduce a family of toric algebras defined by maximal chains of a finite distributive lattice. Applying results on stable set polytopes we conclude that every such algebra is normal and Cohen-Macaulay, and give an interpretation of its…

Let $G$ be a simple graph on the vertex set $\{1,\ldots,n\}$ with $m$ edges. An algebraic object attached to $G$ is the ideal $P_{G}$ generated by diagonal 2-minors of an $n \times n$ matrix of variables. In this paper we prove that if $G$…

We give a criterion for a collection of polynomials to be a universal Gr\"{o}bner basis for an ideal in terms of the multidegree of the closure of the corresponding affine variety in $(\mathbb{P}^1)^N$. This criterion can be used to give…

An ideal I is robust if its universal Gr\"obner basis is a minimal generating set for this ideal. In this paper, we generalize the meaning of robust ideals. An ideal is defined as generalized robust if its universal Gr\"obner basis is equal…

In this paper, we study ideals spanned by polynomials or overconvergent series in a Tate algebra. With state-of-the-art algorithms for computing Tate Gr{\"o}bner bases, even if the input is polynomials, the size of the output grows with the…

We determine a Groebner basis for the secant ideal of the toric ideal associated to the second hypersimplex, with respect to any circular term order. The Groebner basis of the secant ideal requires polynomials of odd degree up to n. This…

We study the three state toric homogeneous Markov chain model and three special cases of it, namely: (i) when the initial state parameters are constant, (ii) without self-loops, and (iii) when both cases are satisfied at the same time.…