Phylogenetic ideals and varieties for the general Markov model

Details Phylogenetic ideals and varieties for the general Markov model Phylogenetic ideals and varieties for the general Markov model

2004-10-28

arxiv.org/abs/math/0410604v2

Mathematics

Algebraic Geometry

5 figures; Minor changes, including renumbering, to reflect final publication form

Scientific paper

The general Markov model of the evolution of biological sequences along a tree leads to a parameterization of an algebraic variety. Understanding this variety and the polynomials, called phylogenetic invariants, which vanish on it, is a problem within the broader area of Algebraic Statistics. For an arbitrary trivalent tree, we determine the full ideal of invariants for the 2-state model, establishing a conjecture of Pachter-Sturmfels. For the $\kappa$-state model, we reduce the problem of determining a defining set of polynomials to that of determining a defining set for a 3-leaved tree. Along the way, we prove several new cases of a conjecture of Garcia-Stillman-Sturmfels on certain statistical models on star trees, and reduce their conjecture to a family of subcases.

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