On the graph labellings arising from phylogenetics

DOI10.2478/S11533-013-0263-3MaRDI QIDQ386402zbMATH OpenOpenAlexFDO

Authors Weronika Buczyńska, Jarosław Buczyński, Kaie Kubjas, Mateusz Michalek

Publication date 9 December 2013

Published in Central European Journal of Mathematics (Search for Journal in Brave)

Copyright license Creative Commons Attribution-NonCommercial-NoDerivs 3.0 Unported

Full work available at URL https://arxiv.org/abs/1105.5382

zbMATH Keywords

2-state Jukes-Cantor modelCavender-Farris-Neyman modelconformal block algebrasgraph labellingsHilbert basislattice conephylogenetic semigroupsemigroup generators

Mathematics Subject Classification ID

Toric varieties, Newton polyhedra, Okounkov bodies (14M25) Lattice polytopes in convex geometry (including relations with commutative algebra and algebraic geometry) (52B20) Applications of commutative algebra (e.g., to statistics, control theory, optimization, etc.) (13P25) Applications of vector bundles and moduli spaces in mathematical physics (twistor theory, instantons, quantum field theory) (14D21) Commutative semigroups (20M14) Free semigroups, generators and relations, word problems (20M05)

Abstract: We study semigroups of labellings associated to a graph. These generalize the Jukes-Cantor model and phylogenetic toric varieties defined by Buczy'nska. Our main theorem bounds the degree of the generators of the semigroup by g+1 when the graph has first Betti number g. Also, we provide a series of examples where the bound is sharp.

Recommendations

• Low degree minimal generators of phylogenetic semigroups
• Phylogenetic toric varieties on graphs
• Enumerating phylogenetic trees with multiple labels
• Toric Ideals of Phylogenetic Invariants
• Toric ideals of homogeneous phylogenetic models

Cites work

• scientific article; zbMATH DE number 572323 (Why is no real title available?)
• scientific article; zbMATH DE number 3366301 (Why is no real title available?)
• Blow-ups of \(\mathbb{P}^{n-3}\) at \(n\) points and spinor varieties
• Bohr-Sommerfeld orbits in the moduli space of flat connections and the Verlinde dimension formula
• Coordinate rings for the moduli stack of \(\mathrm{SL}(\mathbb C)\) quasi-parabolic principal bundles on a curve and toric fiber products
• Fusion rules and modular transformations in 2D conformal field theory
• Geometry of phylogenetic group-based models
• Hilbert polynomial of the Kimura 3-parameter model
• On geometry of binary symmetric models of phylogenetic trees
• Phylogenetic invariants for group-based models
• Phylogenetic toric varieties on graphs
• Sagbi bases of Cox-Nagata rings
• Statistics
• The Magma algebra system. I: The user language
• The algebra of \(\mathrm{SL}_3(\mathbb{C})\) conformal blocks
• Toric Ideals of Phylogenetic Invariants
• Toric geometry of the 3-Kimura model for any tree

Cited in

(9)

• Encodings of cladograms and labeled trees
• Low degree minimal generators of phylogenetic semigroups
• Finite phylogenetic complexity of \(\mathbb{Z}_p\) and invariants for \(\mathbb{Z}_3\)
• Conformal blocks, Berenstein-Zelevinsky triangles, and group-based models
• Compactifications of character varieties and skein relations on conformal blocks
• Semigroup theory of symmetry
• Toric fiber products versus Segre products
• The algebra of \(\mathrm{SL}_3(\mathbb{C})\) conformal blocks
• Phylogeny numbers for graphs with two triangles

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Uses Software

• Magma

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