Toric Ideals of Phylogenetic Invariants
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Publication:4606497
DOI10.1089/CMB.2005.12.204zbMATH Open1391.13058arXivq-bio/0402015OpenAlexW2951723077WikidataQ81522653 ScholiaQ81522653MaRDI QIDQ4606497FDOQ4606497
Authors: Bernd Sturmfels, Seth Sullivant 
Publication date: 8 March 2018
Published in: Journal of Computational Biology (Search for Journal in Brave)
Abstract: Statistical models of evolution are algebraic varieties in the space of joint probability distributions on the leaf colorations of a phylogenetic tree. The phylogenetic invariants of a model are the polynomials which vanish on the variety. Several widely used models for biological sequences have transition matrices that can be diagonalized by means of the Fourier transform of an abelian group. Their phylogenetic invariants form a toric ideal in the Fourier coordinates. We determine generators and Gr"obner bases for these toric ideals. For the Jukes-Cantor and Kimura models on a binary tree, our Gr"obner bases consist of certain explicitly constructed polynomials of degree at most four.
Full work available at URL: https://arxiv.org/abs/q-bio/0402015
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Cited In (72)
- On geometry of binary symmetric models of phylogenetic trees
- Gorenstein property for phylogenetic trivalent trees
- Local equations for equivariant evolutionary models
- Dimensions of group-based phylogenetic mixtures
- Toric geometry of cuts and splits
- Hadamard phylogenetic methods and the \(n\)-taxon process
- Initial ideals of Pfaffian ideals
- Toric varieties in phylogenetics
- Lie-Markov models derived from finite semigroups
- Maximum likelihood estimation of symmetric group-based models via numerical algebraic geometry
- Phylogenetic trees
- When is a polynomial ideal binomial after an ambient automorphism?
- Sagbi bases of Cox-Nagata rings
- Phylogenetic toric varieties on graphs
- Markov bases of conditional independence models for permutations
- Identifiability of 3-class Jukes-Cantor mixtures
- Phylogenetics of Indo-European language families via an algebro-geometric analysis of their syntactic structures
- Geometry of the Kimura 3-parameter model
- Matrix group structure and Markov invariants in the strand symmetric phylogenetic substitution model
- Gaussian tree constraints applied to acoustic linguistic functional data
- Combinatorial degree bound for toric ideals of hypergraphs
- An algebraic analysis of the two state Markov model on tripod trees
- Non-Normal Very Ample Polytopes – Constructions and Examples
- Toric ideals of homogeneous phylogenetic models
- Embeddability of Kimura 3ST Markov matrices
- Relevant phylogenetic invariants of evolutionary models
- Implicit inequality constraints in a binary tree model
- Finite phylogenetic complexity of \(\mathbb{Z}_p\) and invariants for \(\mathbb{Z}_3\)
- Phylogenetic invariants for \(\mathbb{Z}_3\) scheme-theoretically
- On the graph labellings arising from phylogenetics
- Toric geometry of the 3-Kimura model for any tree
- On the ideals of equivariant tree models
- Phylogenetic Networks
- Toric Ideals of Phylogenetic Invariants for the General Group-Based Model on Claw Trees K 1,n
- Preface. Algebraic methods in phylogenetics
- Conformal blocks, Berenstein-Zelevinsky triangles, and group-based models
- Bounded-rank tensors are defined in bounded degree
- Normality of the Kimura 3-Parameter Model
- Binomial fibers and indispensable binomials
- Geometry of phylogenetic group-based models
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- Properties of cut ideals associated to ring graphs
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- Generating Markov evolutionary matrices for a given branch length
- Presentations of semigroup algebras of weighted trees
- Dimensional reduction for the general Markov model on phylogenetic trees
- Neural ideals and stimulus space visualization
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- Finiteness results for abelian tree models
- Low degree equations for phylogenetic group-based models
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- Distinguishing phylogenetic networks
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- Distinguishing level-1 phylogenetic networks on the basis of data generated by Markov processes
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- Low degree minimal generators of phylogenetic semigroups
- Kimura's evolutive model: a linkage between algebra, statistics and biology
- The model-specific Markov embedding problem for symmetric group-based models
- Identifiability in phylogenetics using algebraic matroids
- Maximum likelihood estimation for unrooted 3-leaf trees: an analytic solution for the CFN model
- A novel algebraic approach to time-reversible evolutionary models
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- Nonlinear algebra and applications
- Phylogenetic reconstruction based on algebra
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