Toric ideals of homogeneous phylogenetic models

Abstract

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 ideal of invariants for trees with up to 11 nodes. These are perhaps the first non-trivial Grobner bases calculations in 2^11 indeterminates. We conjecture that there is a quadratic Grobner basis for binary trees. Finally, we give a explicit description of the polytope associated to this toric ideal for an infinite family of binary trees and conjecture that there is a universal bound on the number of vertices of this polytope for binary trees.