On the optimality of the neighbor-joining algorithm 英文参考文献.docVIP

Algorithms for Molecular Biology BioMedCentral Research Open Access On the optimality of the neighbor-joining algorithm Kord Eickmeyer1, Peter Huggins2, Lior Pachter*2 and Ruriko Yoshida3 Address: 1Department of Computer Science, Humboldt University, Unter den Linden 6, 10099 Berlin, Germany , 2Department of Mathematics, University of California at Berkeley Berkeley, CA 94720-3840, USA and 3Department of Statistics, University of Kentucky Lexington, KY 40506, USA Email: Kord Eickmeyer - eickmeye@informatik.hu-berlin.de; Peter Huggins - phuggins@; Lior Pachter* - lpachter@; Ruriko Yoshida - ruriko.yoshida@ * Corresponding author Published: 30 April 2008 Received: 13 November 2007 Accepted: 30 April 2008 Algorithms for Molecular Biology 2008, 3:5 doi:10.1186/1748-7188-3-5 This article is available from: /content/3/1/5 ? 2008 Eickmeyer et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract 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 ? n? ? ? 2 determined by polyhedral subdivisions of the spaces of dissimilarity maps ?+? ? to study the optimality of the neighbor-joining algorithm. In particular, we investigate and compare the polyhedral subdivisions for n≤ 8. This requires the measurement of volumes of spherical polytopes in high dimension, which we obtain using a combination of Monte Carlo methods and polyhedral algorithms. Our results in