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
- scientific article; zbMATH DE number 1865935 (Why is no real title available?)
- Algebraic Statistics for Computational Biology
- Fourier calculus on evolutionary trees
- 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 Ideals of Phylogenetic Invariants
- Toric fiber products
- Toric varieties
Cited in
(24)- Gorenstein property for phylogenetic trivalent trees
- Dimensions of group-based phylogenetic mixtures
- Local equations for equivariant evolutionary models
- Toric varieties in phylogenetics
- Maximum likelihood estimation of symmetric group-based models via numerical algebraic geometry
- Computing algebraic degrees of phylogenetic varieties
- Dimensions of level-1 group-based phylogenetic networks
- Polyhedral computational geometry for averaging metric phylogenetic trees
- The model-specific Markov embedding problem for symmetric group-based models
- 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
- Phylogenetic degrees for claw trees
- Multigraded commutative algebra of graph decompositions
- Normality of the Kimura 3-Parameter Model
- Computing images of polynomial maps
- Lie Markov models with purine/pyrimidine symmetry
- Isotropic models of evolution with symmetries
- H-representation of the Kimura-3 polytope for the \(m\)-claw tree
- Arrangements, matroids and logarithmic vector fields. Abstracts from the workshop held June 16--21, 2024
- Phylogenetic complexity of the Kimura 3-parameter model
- Phylogenetic invariants for group-based models
- Finiteness results for abelian tree models
- Low degree equations for phylogenetic group-based models
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