Facets of the balanced minimal evolution polytope

DOI10.1007/S00285-015-0957-1MaRDI QIDQ304049zbMATH OpenOpenAlexWikidataFDO

Authors Stefan Forcey, Logan Keefe, William Sands

Publication date 23 August 2016

Published in Journal of Mathematical Biology (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/1501.05536

zbMATH Keywords

phylogeneticspolytopefacetsneighbor-joining

Mathematics Subject Classification ID

Linear programming (90C05) Problems related to evolution (92D15) (n)-dimensional polytopes (52B11)

Abstract: A phylogenetic tree is a way to organize a finite set of species, individuals or other sources of related data. The species for which we have existing DNA data make up the set of leaves of the tree. The balanced minimal evolution method of creating phylogenetic trees can be formulated as a linear programming problem, minimizing an inner product over the vertices of the BME polytope. In this paper we undertake the first steps of describing the facets of this polytope.

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Cites work

• scientific article; zbMATH DE number 1945176 (Why is no real title available?)
• All 0-1 polytopes are traveling salesman polytopes
• Approximating the balanced minimum evolution problem
• Computational complexity of inferring phylogenies from dissimilarity matrices
• Optimality of the neighbor joining algorithm and faces of the balanced minimum evolution polytope
• The balanced minimum evolution problem
• polymake: a framework for analyzing convex polytopes

Cited in

(13)

• Optimality of the neighbor joining algorithm and faces of the balanced minimum evolution polytope
• A massively parallel branch-\&-bound algorithm for the balanced minimum evolution problem
• On the balanced minimum evolution polytope
• Galois connections for phylogenetic networks and their polytopes
• On the approximability of the fixed-tree balanced minimum evolution problem
• Level-1 phylogenetic networks and their balanced minimum evolution polytopes
• An information theory perspective on the balanced minimum evolution problem
• Enumerating vertices of the balanced minimum evolution polytope
• Polyhedral geometry of phylogenetic rogue taxa
• Split-facets for balanced minimal evolution polytopes and the permutoassociahedron
• Split network polytopes and network spaces
• A tutorial on the balanced minimum evolution problem
• Polyhedral combinatorics of UPGMA cones

Describes a project that uses

Uses Software

• polymake

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