English

Toric ideals of phylogenetic invariants for the general group-based model on claw trees $K_{1,n}$

Commutative Algebra 2016-08-14 v3 Populations and Evolution

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 Z2\mathbb Z_2 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 Z2\mathbb Z_2 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