Geometry of the Kimura 3-parameter model

DOI10.1016/J.AAM.2007.09.003zbMATH Open1222.14110arXivmath/0702834OpenAlexW2066913767WikidataQ61068404 ScholiaQ61068404MaRDI QIDQ950405FDOQ950405

Marta Casanellas, Jesús Fernández-Sánchez

Publication date: 22 October 2008

Published in: Advances in Applied Mathematics (Search for Journal in Brave)

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.

Full work available at URL: https://arxiv.org/abs/math/0702834

zbMATH Keywords

algebraic statisticslocal complete intersectionphylogenetic invariantsKimura evolutionary model

Mathematics Subject Classification ID

Applications of Markov chains and discrete-time Markov processes on general state spaces (social mobility, learning theory, industrial processes, etc.) (60J20) Problems related to evolution (92D15) Toric varieties, Newton polyhedra, Okounkov bodies (14M25) Complete intersections (14M10)

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Cited In (18)

• Gorenstein property for phylogenetic trivalent trees
• Distance to the stochastic part of phylogenetic varieties
• Local equations for equivariant evolutionary models
• Dimensions of level-1 group-based phylogenetic networks
• Maximum likelihood estimation of symmetric group-based models via numerical algebraic geometry
• Computing the distance to the stochastic part of phylogenetic varieties
• Embeddability of Kimura 3ST Markov matrices
• Equations defining probability tree models
• Relevant phylogenetic invariants of evolutionary models
• Geometry of the Kimura-Georgiou parametrization of modelling filters
• H-Representation of the Kimura-3 Polytope for the $m$-Claw Tree
• On the ideals of equivariant tree models
• On the geometry arising in some meteorological models in two and three dimensions
• Normality of the Kimura 3-Parameter Model
• Klein-Beltrami model. III
• Phylogenetic complexity of the Kimura 3-parameter model
• Finiteness results for abelian tree models
• Low degree equations for phylogenetic group-based models

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