Skip Navigation

This Article
Right arrow FREE Full Text (PDF) Freely available
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in ISI Web of Science
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Search for citing articles in:
ISI Web of Science (14)
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Pearson, W. R.
Right arrow Articles by Zhang, T.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Pearson, W. R.
Right arrow Articles by Zhang, T.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Molecular Biology and Evolution, Vol 16, 806-816, Copyright © 1999 by Society for Molecular Biology and Evolution

ORIGINAL ARTICLE

Generalized neighbor-joining: more reliable phylogenetic tree reconstruction

WR Pearson, G Robins and T Zhang
Department of Computer Science, University of Virginia, USA. wrp@virginia.edu

We have developed a phylogenetic tree reconstruction method that detects and reports multiple topologically distant low-cost solutions. Our method is a generalization of the neighbor-joining method of Saitou and Nei and affords a more thorough sampling of the solution space by keeping track of multiple partial solutions during its execution. The scope of the solution space sampling is controlled by a pair of user- specified parameters--the total number of alternate solutions and the number of alternate solutions that are randomly selected--effecting a smooth trade-off between run time and solution quality and diversity. This method can discover topologically distinct low-cost solutions. In tests on biological and synthetic data sets using either the least- squares distance or minimum-evolution criterion, the method consistently performed as well as, or better than, both the neighbor- joining heuristic and the PHYLIP implementation of the Fitch-Margoliash distance measure. In addition, the method identified alternative tree topologies with costs within 1% or 2% of the best, but with topological distances of 9 or more partitions from the best solution (16 taxa); with 32 taxa, topologies were obtained 17 (least-squares) and 22 (minimum-evolution) partitions from the best topology when 200 partial solutions were retained. Thus, the method can find lower-cost tree topologies and near-best tree topologies that are significantly different from the best topology.
Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 CSH ProtocolsHome page
D. W. Mount
Distance Methods for Phylogenetic Prediction
CSH Protocols, April 1, 2008; 2008(5): pdb.top33 - pdb.top33.
[Abstract] [Full Text]

Home page
 J. Gen. Virol.Home page
N. N. Zheng, C. Vella, P. J. Easterbrook, and R. S. Daniels
Selection following isolation of human immunodeficiency virus type 1 in peripheral blood mononuclear cells and herpesvirus saimiri-transformed T cells is comparable
J. Gen. Virol., June 1, 2002; 83(6): 1343 - 1352.
[Abstract] [Full Text] [PDF]


Disclaimer:
Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.