On the graph labellings arising from phylogenetics

DOI10.2478/S11533-013-0263-3zbMATH Open1282.14087arXiv1105.5382OpenAlexW3098434817MaRDI QIDQ386402FDOQ386402

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)

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.

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

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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)

Cites Work

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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
• Toric fiber products versus Segre products
• Semigroup theory of symmetry
• The algebra of \(\mathrm{SL}_3(\mathbb{C})\) conformal blocks
• Phylogeny numbers for graphs with two triangles

Uses Software

• Magma

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