Journal of Molecular Evolution

, Volume 62, Issue 6, pp 785–792

Relaxed Neighbor Joining: A Fast Distance-Based Phylogenetic Tree Construction Method

Authors

    • Department of Biological SciencesUniversity of Idaho
  • Luke Sheneman
    • Department of Biological SciencesUniversity of Idaho
  • James Foster
    • Department of Biological SciencesUniversity of Idaho
Article

DOI: 10.1007/s00239-005-0176-2

Cite this article as:
Evans, J., Sheneman, L. & Foster, J. J Mol Evol (2006) 62: 785. doi:10.1007/s00239-005-0176-2

Abstract

Our ability to construct very large phylogenetic trees is becoming more important as vast amounts of sequence data are becoming readily available. Neighbor joining (NJ) is a widely used distance-based phylogenetic tree construction method that has historically been considered fast, but it is prohibitively slow for building trees from increasingly large datasets. We developed a fast variant of NJ called relaxed neighbor joining (RNJ) and performed experiments to measure the speed improvement over NJ. Since repeated runs of the RNJ algorithm generate a superset of the trees that repeated NJ runs generate, we also assessed tree quality. RNJ is dramatically faster than NJ, and the quality of resulting trees is very similar for the two algorithms. The results indicate that RNJ is a reasonable alternative to NJ and that it is especially well suited for uses that involve large numbers of taxa or highly repetitive procedures such as bootstrapping.

Keywords

Phylogenetic tree constructionNeighbor joiningDistance method

Copyright information

© Springer Science+Business Media, Inc. 2006