Toric geometry of the Cavender-Farris-Neyman model with a molecular clock

DOI10.1016/j.aam.2020.102119zbMath1457.92125arXiv1805.04175OpenAlexW3095043579MaRDI QIDQ2221783

Seth Sullivant, Jane Ivy Coons

Publication date: 2 February 2021

Published in: Advances in Applied Mathematics (Search for Journal in Brave)

Full work available at URL: https://arxiv.org/abs/1805.04175

zbMATH Keywords

molecular clocktoric idealCavender-Farris-Neyman modelrooted binary phylogenetic tree

Mathematics Subject Classification ID

Problems related to evolution (92D15) Toric varieties, Newton polyhedra, Okounkov bodies (14M25) Biological rhythms and synchronization (92B25) Algebraic statistics (62R01)

Related Items (3)

The \(h^\ast\)-polynomial of the order polytope of the zig-zag poset ⋮ Nonlinear algebra and applications ⋮ Invariants for level-1 phylogenetic networks under the Cavendar-Farris-Neyman model

Uses Software

• OEIS

Cites Work

• Sagbi bases of Cox-Nagata rings
• Two poset polytopes
• Spectral analysis of phylogenetic data
• A note on the metric properties of trees
• Invariants of some probability models used in phylogenetic inference
• Toric fiber products
• On geometry of binary symmetric models of phylogenetic trees
• A Survey of Alternating Permutations
• Computing the Continuous Discretely
• Lectures on Polytopes
• Algebraic Statistics
• Toric Ideals of Phylogenetic Invariants
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