The neighbor-net algorithm

DOI10.1016/j.aam.2010.09.002zbMath1274.92005arXivmath/0702515OpenAlexW2128686408MaRDI QIDQ550258

Dan Levy, Lior Pachter

Publication date: 8 July 2011

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

Full work available at URL: https://arxiv.org/abs/math/0702515

zbMATH Keywords

traveling salesman problemneighbor-joiningminimum evolutionbalanced lengthcircular decomposable metricKalmanson conditionsneighbor-netsplits network

Mathematics Subject Classification ID

Applications of statistics to biology and medical sciences; meta analysis (62P10) Problems related to evolution (92D15) Taxonomy, cladistics, statistics in mathematical biology (92B10) Combinatorics in computer science (68R05) Algebraic combinatorics (05E99)

Related Items (7)

Circular Planar Electrical Networks, Split Systems, and Phylogenetic Networks ⋮ The dual complex of \({\overline{M}_{0,n}}\) via phylogenetics ⋮ Expansion of gene clusters, circular orders, and the shortest Hamiltonian path problem ⋮ A Space of Phylogenetic Networks ⋮ Affine and projective tree metric theorems ⋮ Level-1 phylogenetic networks and their balanced minimum evolution polytopes ⋮ Fishing for minimum evolution trees with neighbor-nets

Uses Software

• TSPLIB
• Concorde
• BIONJ

Cites Work

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• Toric geometry of cuts and splits
• Why neighbor-joining works
• The performance of neighbor-joining methods of phylogenetic reconstruction
• A canonical decomposition theory for metrics on a finite set
• A note on circular decomposable metrics
• Geometry of the space of phylogenetic trees
• Cyclic permutations and evolutionary trees
• \(T\)-theory: An overview
• The number of clone orderings
• When the greedy algorithm fails
• Coxeter complexes and graph-associahedra
• TSPLIB—A Traveling Salesman Problem Library
• A Note On Kalmanson Matrices^∗
• Sometimes Travelling is Easy: The Master Tour Problem
• Extending Tree Models to Splits Networks
• Small Trees and Generalized Neighbor-Joining
• Edgeconvex Circuits and the Traveling Salesman Problem
• Algebraic Statistics for Computational Biology
• Automata, Languages and Programming

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