Geometry of phylogenetic group-based models
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Abstract: In this paper we complete the results of Sullivant and Sturmfels proving that many of the algebraic group-based models for Markov processes on trees are pseudo-toric. We also show in which cases these varieties are normal. This is done by the generalization of the discrete Fourier transform approach. In the next step, following Sullivant and Sturmfels, we describe a fast algorithm finding a polytope associated to these algebraic models. However in our case we apply the notions of sockets and networks extending the work of Buczynska and Wisniewski who introduced it for the binary case.
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- Finite phylogenetic complexity of \(\mathbb{Z}_p\) and invariants for \(\mathbb{Z}_3\)
- Finite phylogenetic complexity and combinatorics of tables
- Phylogenetic invariants for \(\mathbb{Z}_3\) scheme-theoretically
Cites work
- Algebraic Statistics for Computational Biology
- Fourier calculus on evolutionary trees
- scientific article; zbMATH DE number 1865935 (Why is no real title available?)
- Introduction to Toric Varieties. (AM-131)
- Invariants of phylogenies in a simple case with discrete states
- Invariants of some probability models used in phylogenetic inference
- Isotropic models of evolution with symmetries
- On geometry of binary symmetric models of phylogenetic trees
- On the ideals of equivariant tree models
- Phylogenetic algebraic geometry
- Sagbi bases of Cox-Nagata rings
- Toric fiber products
- Toric Ideals of Phylogenetic Invariants
- Toric varieties
Cited in
(26)- Phylogenetic complexity of the Kimura 3-parameter model
- Dimensions of group-based phylogenetic mixtures
- Maximum likelihood estimation of symmetric group-based models via numerical algebraic geometry
- The model-specific Markov embedding problem for symmetric group-based models
- Multigraded commutative algebra of graph decompositions
- Lie Markov models with purine/pyrimidine symmetry
- Computing images of polynomial maps
- Finiteness results for abelian tree models
- Low degree equations for phylogenetic group-based models
- Polyhedral computational geometry for averaging metric phylogenetic trees
- Local equations for equivariant evolutionary models
- Gorenstein property for phylogenetic trivalent trees
- Phylogenetic invariants for group-based models
- Toric varieties in phylogenetics
- Finite phylogenetic complexity of \(\mathbb{Z}_p\) and invariants for \(\mathbb{Z}_3\)
- Phylogenetic invariants for \(\mathbb{Z}_3\) scheme-theoretically
- Isotropic models of evolution with symmetries
- On the graph labellings arising from phylogenetics
- Normality of the Kimura 3-Parameter Model
- H-representation of the Kimura-3 polytope for the m-claw tree
- Brownian motion tree models are toric
- Phylogenetic degrees for claw trees
- Dimensions of level-1 group-based phylogenetic networks
- Computing algebraic degrees of phylogenetic varieties
- Arrangements, matroids and logarithmic vector fields. Abstracts from the workshop held June 16--21, 2024
- Computing implicitizations of multi-graded polynomial maps
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