The generating conjecture for homogeneous invariants of the 2-state GM+I model

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Let TT be an nn-taxon binary tree, and let p11…1p_{11\dots1} and p22…2p_{22\dots2} denote the joint-distribution coordinates in which every state is respectively 11 and 22. Consider the edge flattenings of the joint-distribution tensor, their 3×33\times 3 minors, and the stochastic invariant for the 2-state general Markov model with invariable sites (GM+I).

Generating conjecture. The ideal of homogeneous invariants for the 2-state GM+I model on TT is generated by those 3×33\times 3 minors of edge flattenings that do not involve the variables p11…1p_{11\dots1} and p22…2p_{22\dots2}, together with the stochastic invariant.

This gives a proposed complete generating set for the homogeneous phylogenetic ideal of the 2-state GM+I model on every binary tree, extending the known edge-flattening invariants while accounting for the two all-equal-state coordinates.

References

Primary source

Elizabeth S. Allman and John A. Rhodes, “Identifying evolutionary trees and substitution parameters for the general Markov model with invariable sites”, arXiv:q-bio/0702050 (2007).

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