2007/10/26 by Kord Eickmeyer, Peter Huggins, Eickmeyer, Kord +5
Agricultural and Biological Sciences · Biochemistry, Genetics and Molecular Biology · Earth and Planetary Sciences · #Chromosomal and Genetic Variations #Evolution and Paleontology Studies #FOS: Biological sciences #Genomics and Phylogenetic Studies #Populations and Evolution (q-bio.PE) #Quantitative Methods (q-bio.QM)
paper · pdf · doi:10.48550/arxiv.0710.5142
openalex publication_date 2007/10/26 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/28
The popular neighbor-joining (NJ) algorithm used in phylogenetics is a greedy algorithm for finding the balanced minimum evolution (BME) tree associated to a dissimilarity map. From this point of view, NJ is ``optimal'' when the algorithm outputs the tree which minimizes the balanced minimum evolution criterion. We use the fact that the NJ tree topology and the BME tree topology are determined by polyhedral subdivisions of the spaces of dissimilarity maps \R+n \choose 2 to study the optimality of the neighbor-joining algorithm. In particular, we investigate and compare the polyhedral subdivisions for n ≤ 8. A key requirement is the measurement of volumes of spherical polytopes in high dimension, which we obtain using a combination of Monte Carlo methods and polyhedral algorithms. We show that highly unrelated trees can be co-optimal in BME reconstruction, and that NJ regions are not convex. We obtain the l2 radius for neighbor-joining for n=5 and we conjecture that the ability of the neighbor-joining algorithm to recover the BME tree depends on the diameter of the BME tree.