Related papers: Local description of phylogenetic group-based mode…
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 present geometric features of group based models. We focus on the 3-Kimura model. We present a precise geometric description of the variety associated to any tree on a Zariski open set. In particular this set contains all…
Group-based models arise in algebraic statistics while studying evolution processes. They are represented by embedded toric algebraic varieties. Both from the theoretical and applied point of view one is interested in determining the ideals…
A phylogenetic variety is an algebraic variety parameterized by a statistical model of the evolution of biological sequences along a tree. Understanding this variety is an important problem in the area of algebraic statistics with…
In this paper we improve our previous results on classification of groups of points on abelian varieties over finite fields. The classification is given in terms of the Weil polynomial of abelian varieties in a given $k$-isogeny class.
Let $A$ be an abelian variety with commutative endomorphism algebra over a finite field $k$. The $k$-isogeny class of $A$ is uniquely determined by a Weil polynomial $f_A$ without multiple roots. We give a classification of the groups of…
In this paper we provide an algorithm to classify groups of points on abelian threefolds over finite fields. The classification is given in terms of the Weil polynomial of abelian varieties in a given $\mathbb{F}_q$-isogeny class. This work…
We provide a complete classification of normal phylogenetic varieties coming from tripods, and more generally, from trivalent trees. Let $G$ be an abelian group. We prove that the group-based phylogenetic variety $X_{G,\mathcal{T}}$, for…
We study the groups of rational points of abelian varieties defined over a finite field $ \mathbb{F}_q$ whose endomorphism rings are commutative, or, equivalently, whose isogeny classes are determined by squarefree characteristic…
In this paper, we classify the possible group structures on the set of $R$-valued points of an abelian variety, where $R$ is any real closed field. We make use of a family of abelian varieties that, in effect, allows one to quantify over…
The Kimura 3-parameter model on a tree of n leaves is one of the most used in phylogenetics. The affine algebraic variety W associated to it is a toric variety. We study its geometry and we prove that it is isomorphic to a geometric…
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…
Let $A$ be an abelian variety over a finite field $k$. The $k$-isogeny class of $A$ is uniquely determined by the Weil polynomial $f_A$. We assume that $f_A$ is separable. For a given prime number $\ell\neq\mathrm{char}\, k$ we give a…
Group-based models appear in algebraic statistics as mathematical models coming from evolutionary biology, respectively the study of mutations of organisms. Both theoretically and in terms of applications, we are interested in determining…
We study phylogenetic complexity of finite abelian groups - an invariant introduced by Sturmfels and Sullivant. The invariant is hard to compute - so far it was only known for $Z_2$, in which case it equals $2$. We prove that phylogenetic…
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.…
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…
Given an abelian variety $A$ defined over a finite field $k$, we say that $A$ is "cyclic" if its group $A(k)$ of rational points is cyclic. In this paper we give a bijection between cyclic abelian varieties of an ordinary isogeny class…
We estimate the fraction of isogeny classes of abelian varieties over a finite field which have a given characteristic polynomial P(T) modulo l. As an application we find the proportion of isogeny classes of abelian varieties with a…
Consider the algebraic dynamics on a torus T=G_m^n given by a matrix M in GL_n(Z). Assume that the characteristic polynomial of M is prime to all polynomials X^m-1. We show that any finite equivariant map from another algebraic dynamics…