Related papers: Toric ideals of homogeneous phylogenetic models

We propose an effective algorithm that decides if a prime ideal in a polynomial ring over the complex numbers can be transformed into a toric ideal by a linear automorphism of the ambient space. If this is the case, the algorithm computes…

In the last decade, some algebraic tools have been successfully applied to phylogenetic reconstruction. These tools are mainly based on the knowledge of equations describing algebraic varieties associated to phylogenetic trees evolving…

This paper investigates the Poisson geometry associated to a cluster algebra over the complex numbers, and its relationship to compatible torus actions. We show, under some assumptions, that each Noetherian cluster algebra has only finitely…

Recently there have been several attempts to provide a whole set of generators of the ideal of the algebraic variety associated to a phylogenetic tree evolving under an algebraic model. These algebraic varieties have been proven to be…

An order-theoretic forest is a countable partial order such that the set of elements larger than any element is linearly ordered. It is an order-theoretic tree if any two elements have an upper-bound. The order type of a branch can be any…

We study how to lift Markov bases and Gr\"obner bases along linear maps of lattices. We give a lifting algorithm that allows to compute such bases iteratively provided a certain associated semigroup is normal. Our main application is the…

Let K be a field and let m_0,...,m_{n} be an almost arithmetic sequence of positive integers. Let C be a toric variety in the affine (n+1)-space, defined parametrically by x_0=t^{m_0},...,x_{n}=t^{m_{n}}. In this paper we produce a minimal…

A major task of evolutionary biology is the reconstruction of phylogenetic trees from molecular data. The evolutionary model is given by a Markov chain on a tree. Given samples from the leaves of the Markov chain, the goal is to reconstruct…

We consider arrangements of tropical hyperplanes where the apices of the hyperplanes are taken to infinity in certain directions. Such an arrangement defines a decomposition of Euclidean space where a cell is determined by its `type' data,…

In this paper we investigate properties of algebraic varieties representing group-based phylogenetic models. We propose a method of generating many phylogenetic invariants. We prove that we obtain all invariants for any tree for the binary…

In this paper we develop a Grobner bases theory for ideals of partial difference polynomials with constant or non-constant coefficients. In particular, we introduce a criterion providing the finiteness of such bases when a difference ideal…

Let $I_1\subset I_2\subset\dots$ be an increasing sequence of ideals of the ring $\Bbb Z[X]$, $X=(x_1,\dots,x_n)$ and let $I$ be their union. We propose an algorithm to compute the Gr\"obner base of $I$ under the assumption that the…

The toric fiber product is a general procedure for gluing two ideals, homogeneous with respect to the same multigrading, to produce a new homogeneous ideal. Toric fiber products generalize familiar constructions in commutative algebra like…

In this paper we present with algebraic trees a novel notion of (continuum) trees which generalizes countable graph-theoretic trees to (potentially) uncountable structures. For that purpose we focus on the tree structure given by the branch…

By the classical result of Milnor and Novikov, the unitary cobordism ring is isomorphic to a graded polynomial ring with countably many generators: $\Omega^U_*\simeq \mathbb Z[a_1,a_2,\dots]$, ${\rm deg}(a_i)=2i$. In this paper we solve a…

For an arbitrary field K, let I be an ideal in the ring K[[x,y]] expressible as a polynomial in either the pair of ideals (x, y^4) and (x,y) or the pair (x,y^3) and (x^2, y). Let G be the group of automorphisms of K[[x,y]] sending the ideal…

Hara, Takemura and Yoshida discuss toric ideals arising from two way subtable sum problems and shows that these toric ideals are generated by quadratic binomials if and only if the subtables are either diagonal or triangular. In the present…

It has remained an open question for some time whether, given a set of not necessarily binary (i.e. "nonbinary") trees T on a set of taxa X, it is possible to determine in time f(r).poly(m) whether there exists a phylogenetic network that…

In 1980, White conjectured that the toric ideal associated to a matroid is generated by binomials corresponding to a symmetric exchange. In this paper, we prove that classes of matroids for which the toric ideal is generated by quadrics and…

Rooted binary perfect phylogenies provide a generalization of rooted binary unlabeled trees in which each leaf is assigned a positive integer value that corresponds in a biological setting to the count of the number of indistinguishable…