Phylogenetic invariants for the general Markov model of sequence mutation.

A phylogenetic invariant for a model of biological sequence evolution along a phylogenetic tree is a polynomial that vanishes on the expected frequencies of base patterns at the terminal taxa. While the use of these invariants for phylogenetic inference has long been of interest, explicitly constructing such invariants has been problematic. We construct invariants for the general Markov model of kappa-base sequence evolution on an n-taxon tree, for any kappa and n. The method depends primarily on the observation that certain matrices defined in terms of expected pattern frequencies must commute, and yields many invariants of degree kappa+1, regardless of the value of n. We define strong and parameter-strong sets of invariants, and prove several theorems indicating that the set of invariants produced here has these properties on certain sets of possible pattern frequencies. Thus our invariants may be sufficient for phylogenetic applications.