Related papers: Phylogenetic toric varieties on graphs
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…
It is known that isomorphisms of graph Jacobians induce cyclic bijections on the associated graphs. We characterize when such cyclic bijections can be strengthened to graph isomorphisms, in terms of an easily computed divisor. The result…
Phylogenetic invariants are certain polynomials in the joint probability distribution of a Markov model on a phylogenetic tree. Such polynomials are of theoretical interest in the field of algebraic statistics and they are also of practical…
We consider the phylogenetic tree model in which every node of the tree is observed and binary and the transitions are given by the same matrix on each edge of the tree. We are able to compute the Grobner basis and Markov basis of the toric…
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…
Phylogenetic algebraic geometry is concerned with certain complex projective algebraic varieties derived from finite trees. Real positive points on these varieties represent probabilistic models of evolution. For small trees, we recover…
We compute the divisor class group and the Picard group of projective varieties with Hibi rings as homogeneous coordinate rings. These varieties are precisely the toric varieties associated to order polytopes. We use tools from the theory…
Phylogenetic trees are the fundamental mathematical representation of evolutionary processes in biology. They are also objects of interest in pure mathematics, such as algebraic geometry and combinatorics, due to their discrete geometry.…
Associated to any graph is a toric ideal whose generators record relations among the cuts of the graph. We study these ideals and the geometry of the corresponding toric varieties. Our theorems and conjectures relate the combinatorial…
Phylogenetic networks represent evolutionary history of species and can record natural reticulate evolutionary processes such as horizontal gene transfer and gene recombination. This makes phylogenetic networks a more comprehensive…
A {\em cyclic graph} is a graph with at each vertex a cyclic order of the edges incident with it specified. We characterize which real-valued functions on the collection of cubic cyclic graphs are partition functions of a real vertex model…
We investigate Gauss maps of (not necessarily normal) projective toric varieties over an algebraically closed field of arbitrary characteristic. The main results are as follows: (1) The structure of the Gauss map of a toric variety is…
Phylogenetic trees are simple models of evolutionary processes. They describe conditionally independent divergent evolution of taxa from common ancestors. Phylogenetic trees commonly do not have enough flexibility to adequately model all…
In this thesis we study toric degenerations of projective varieties. We compare different constructions to understand how and why they are related as s first step towards developing a global framework. In focus are toric degenerations…
In mathematical phylogenetics, evolutionary relationships are often represented by trees and networks. The latter are typically used whenever the relationships cannot be adequately described by a tree, which happens when so-called…
Given a finite, simple, vertex-weighted graph, we construct a graded associative (non-commutative) algebra, whose generators correspond to vertices and whose ideal of relations has generators that are graded commutators corresponding to…
This is an expository paper in which we define projective GIT quotients and introduce toric varieties from this perspective. It is intended primarily for readers who are learning either invariant theory or toric geometry for the first time.
Phylogenetics is the study of the evolutionary relationships between organisms. One of the main challenges in the field is to take biological data for a group of organisms and to infer an evolutionary tree, a graph that represents these…
We study phylogenetic invariants of models of evolution whose group of symmetries is the cyclic group with 3 elements. We prove that projective schemes corresponding to the ideal I of phylogenetic invariants of such a model and to its…
If (Q,A) is a marked polygon with one interior point, then a general polynomial f in K[x,y] with support A defines an elliptic curve C on the toric surface X_A. If K has a non-archimedean valuation into the real numbers we can tropicalize C…