Toric Ideals of Phylogenetic Invariants
From MaRDI portal
Publication:4606497
DOI10.1089/cmb.2005.12.204zbMath1391.13058arXivq-bio/0402015OpenAlexW2951723077WikidataQ81522653 ScholiaQ81522653MaRDI QIDQ4606497
Bernd Sturmfels, Seth Sullivant
Publication date: 8 March 2018
Published in: Journal of Computational Biology (Search for Journal in Brave)
Full work available at URL: https://arxiv.org/abs/q-bio/0402015
Toric varieties, Newton polyhedra, Okounkov bodies (14M25) Applications of commutative algebra (e.g., to statistics, control theory, optimization, etc.) (13P25)
Related Items (56)
Phylogenetic trees ⋮ Local equations for equivariant evolutionary models ⋮ Non-Normal Very Ample Polytopes – Constructions and Examples ⋮ Topics on phylogenetic algebraic geometry ⋮ Matrix group structure and Markov invariants in the strand symmetric phylogenetic substitution model ⋮ Toric geometry of cuts and splits ⋮ Hadamard phylogenetic methods and the \(n\)-taxon process ⋮ Properties of cut ideals associated to ring graphs ⋮ Finite phylogenetic complexity of \(\mathbb{Z}_p\) and invariants for \(\mathbb{Z}_3\) ⋮ Phylogenetic invariants for \(\mathbb{Z}_3\) scheme-theoretically ⋮ Embeddability of Kimura 3ST Markov matrices ⋮ Distinguishing Phylogenetic Networks ⋮ Gorenstein property for phylogenetic trivalent trees ⋮ On the graph labellings arising from phylogenetics ⋮ H-Representation of the Kimura-3 Polytope for the $m$-Claw Tree ⋮ Initial ideals of Pfaffian ideals ⋮ Generating Markov evolutionary matrices for a given branch length ⋮ Neural ideals and stimulus space visualization ⋮ Binomial fibers and indispensable binomials ⋮ Nonlinear algebra and applications ⋮ Invariants for level-1 phylogenetic networks under the Cavendar-Farris-Neyman model ⋮ Phylogenetic Networks ⋮ An algebraic analysis of the two state Markov model on tripod trees ⋮ Implicit inequality constraints in a binary tree model ⋮ Unnamed Item ⋮ Phylogenetic complexity of the Kimura 3-parameter model ⋮ Bounded-rank tensors are defined in bounded degree ⋮ Toric geometry of the Cavender-Farris-Neyman model with a molecular clock ⋮ Conformal blocks, Berenstein-Zelevinsky triangles, and group-based models ⋮ Geometry of phylogenetic group-based models ⋮ Phylogenetic invariants for stationary base composition ⋮ Identifiability in phylogenetics using algebraic matroids ⋮ Distinguishing level-1 phylogenetic networks on the basis of data generated by Markov processes ⋮ The model-specific Markov embedding problem for symmetric group-based models ⋮ Preface. Algebraic methods in phylogenetics ⋮ Dimensions of group-based phylogenetic mixtures ⋮ Maximum likelihood estimation of symmetric group-based models via numerical algebraic geometry ⋮ Lie-Markov models derived from finite semigroups ⋮ Toric fiber products ⋮ On geometry of binary symmetric models of phylogenetic trees ⋮ Conjunctive Bayesian networks ⋮ Geometry of the Kimura 3-parameter model ⋮ Phylogenetic ideals and varieties for the general Markov model ⋮ Phylogenetic mixtures and linear invariants for equal input models ⋮ Identifiability of 3-class Jukes-Cantor mixtures ⋮ Sagbi bases of Cox-Nagata rings ⋮ When is a polynomial ideal binomial after an ambient automorphism? ⋮ Dimensional reduction for the general Markov model on phylogenetic trees ⋮ Relevant phylogenetic invariants of evolutionary models ⋮ Gaussian tree constraints applied to acoustic linguistic functional data ⋮ Computing images of polynomial maps ⋮ On the ideals of equivariant tree models ⋮ Phylogenetics of Indo-European language families via an algebro-geometric analysis of their syntactic structures ⋮ Normality of the Kimura 3-Parameter Model ⋮ COMBINATORIAL DEGREE BOUND FOR TORIC IDEALS OF HYPERGRAPHS ⋮ Low degree equations for phylogenetic group-based models
Uses Software
This page was built for publication: Toric Ideals of Phylogenetic Invariants
