Geometry of the space of phylogenetic trees

DOI10.1006/AAMA.2001.0759zbMath0995.92035DBLPjournals/aam/BilleraHV01OpenAlexW4210681352WikidataQ58803813 ScholiaQ58803813MaRDI QIDQ1604344

Karen Vogtmann, Susan P. Holmes, Billera, Louis J.

Publication date: 4 July 2002

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

Full work available at URL: https://doi.org/10.1006/aama.2001.0759

zbMATH Keywords

bootstrapgeodesicsCAT(0) spaceconsensusphylogenetic treesassociahedronsemi-labeled trees

Mathematics Subject Classification ID

Trees (05C05) Problems related to evolution (92D15) Applications of graph theory (05C90)

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Uses Software

• PHYLIP

Cites Work

• Matching theory
• The Steiner problem in phylogeny is NP-complete
• Recovering symbolically dated, rooted trees from symbolic ultrametrics
• Nonpositive curvature of blow-ups
• Nonlinear Markov operators, discrete heat flow, and harmonic maps between singular spaces
• The permutoassociahedron, Mac Lane's coherence theorem and asymptotic zones for the KZ equation
• The associahedron and triangulations of the \(n\)-gon
• Nonlinear martingale theory for processes with values in metric spaces of nonpositive curvature
• The tree representation of \(\Sigma_{n+1}\)
• Reductive groups over a local field
• NON-NULL RANKING MODELS. I
• Statistical Inference of Phylogenies
• Local structure of some Out(F_n)-complexes
• Rotation Distance, Triangulations, and Hyperbolic Geometry
• Short Encodings of Evolving Structures
• Matchings and phylogenetic trees
• Bootstrap confidence levels for phylogenetic trees
• Homotopy Associativity of H-Spaces. I
• Unnamed Item
• Unnamed Item
• Unnamed Item
• Unnamed Item
• Unnamed Item
• Unnamed Item
• Unnamed Item
• Unnamed Item
• Unnamed Item
• Unnamed Item
• Unnamed Item
• Unnamed Item
• Unnamed Item

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