Toric ideals of phylogenetic invariants for the general group-based model on claw trees $K_{1,n}$
Abstract
We address the problem of studying the toric ideals of phylogenetic invariants for a general group-based model on an arbitrary claw tree. We focus on the group and choose a natural recursive approach that extends to other groups. The study of the lattice associated with each phylogenetic ideal produces a list of circuits that generate the corresponding lattice ideal. In addition, we describe explicitly a quadratic lexicographic Gr\"{o}bner basis of the toric ideal of invariants for the claw tree on an arbitrary number of leaves. Combined with a result of Sturmfels and Sullivant, this implies that the phylogenetic ideal of every tree for the group has a quadratic Gr\"{o}bner basis. Hence, the coordinate ring of the toric variety is a Koszul algebra.
Keywords
Cite
@article{arxiv.math/0702368,
title = {Toric ideals of phylogenetic invariants for the general group-based model on claw trees $K_{1,n}$},
author = {Julia Chifman and Sonja Petrović},
journal= {arXiv preprint arXiv:math/0702368},
year = {2016}
}
Comments
Revised introduction (more complete); revised algorithms; added references. To appear in Proceedings of Algebraic Biology 2007