Geometry of the Kimura 3-parameter model
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Abstract: The Kimura 3-parameter model on a tree of n leaves is one of the most used in phylogenetics. The affine algebraic variety W associated to it is a toric variety. We study its geometry and we prove that it is isomorphic to a geometric quotient of the affine space by a finite group acting on it. As a consequence, we are able to study the singularities of W and prove that the biologically meaningful points are smooth points. Then we give an algorithm for constructing a set of minimal generators of the localized ideal at these points, for an arbitrary number of leaves n. This leads to a major improvement of phylogenetic reconstruction methods based on algebraic geometry.
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Cited in
(21)- Distance to the stochastic part of phylogenetic varieties
- Local equations for equivariant evolutionary models
- Embeddability of Kimura 3ST Markov matrices
- H-representation of the Kimura-3 polytope for the \(m\)-claw tree
- Hilbert polynomial of the Kimura 3-parameter model
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- U(1) ×U(1) ×U(1) symmetry of the Kimura 3ST model and phylogenetic branching processes
- Dimensions of level-1 group-based phylogenetic networks
- On the geometry arising in some meteorological models in two and three dimensions
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- Gorenstein property for phylogenetic trivalent trees
- Normality of the Kimura 3-Parameter Model
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- Low degree equations for phylogenetic group-based models
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