Geometry of phylogenetic group-based models

DOI10.1016/J.JALGEBRA.2011.05.016zbMATH Open1251.14040arXiv1004.3012OpenAlexW1544767054MaRDI QIDQ663592FDOQ663592

Authors: Mateusz Michalek 

Publication date: 25 February 2012

Published in: Journal of Algebra (Search for Journal in Brave)

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.

Full work available at URL: https://arxiv.org/abs/1004.3012

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• H-representation of the Kimura-3 polytope for the \(m\)-claw tree
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zbMATH Keywords

toric varietiesG-modelsgroup-based modelsphylogenetic varieties

Mathematics Subject Classification ID

Applications of statistics to biology and medical sciences; meta analysis (62P10) Problems related to evolution (92D15) Taxonomy, cladistics, statistics in mathematical biology (92B10) Toric varieties, Newton polyhedra, Okounkov bodies (14M25)

Cites Work

• Title not available (Why is that?)
• Algebraic Statistics for Computational Biology
• Introduction to Toric Varieties. (AM-131)
• Toric varieties
• Sagbi bases of Cox-Nagata rings
• Phylogenetic algebraic geometry
• On the ideals of equivariant tree models
• Invariants of phylogenies in a simple case with discrete states
• Fourier calculus on evolutionary trees
• Invariants of some probability models used in phylogenetic inference
• Toric Ideals of Phylogenetic Invariants
• Toric fiber products
• On geometry of binary symmetric models of phylogenetic trees
• Isotropic models of evolution with symmetries

Cited In (24)

• Gorenstein property for phylogenetic trivalent trees
• Local equations for equivariant evolutionary models
• Dimensions of group-based phylogenetic mixtures
• Computing algebraic degrees of phylogenetic varieties
• Dimensions of level-1 group-based phylogenetic networks
• Toric varieties in phylogenetics
• Maximum likelihood estimation of symmetric group-based models via numerical algebraic geometry
• Polyhedral computational geometry for averaging metric phylogenetic trees
• The model-specific Markov embedding problem for symmetric group-based models
• Phylogenetic degrees for claw trees
• Finite phylogenetic complexity of \(\mathbb{Z}_p\) and invariants for \(\mathbb{Z}_3\)
• Phylogenetic invariants for \(\mathbb{Z}_3\) scheme-theoretically
• Multigraded commutative algebra of graph decompositions
• On the graph labellings arising from phylogenetics
• Normality of the Kimura 3-Parameter Model
• Computing images of polynomial maps
• Isotropic models of evolution with symmetries
• Lie Markov models with purine/pyrimidine symmetry
• Arrangements, matroids and logarithmic vector fields. Abstracts from the workshop held June 16--21, 2024
• H-representation of the Kimura-3 polytope for the \(m\)-claw tree
• 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

Uses Software

• Macaulay2

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