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.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
References
Bruno WJ, Socci ND, Halpern AL (2000) Weighted neighbor joining: a likelihood-based approach to distance-based phylogeny reconstruction. Mol Biol Evol 17:189–197
Chase MW, Soltis DE, Olmstead RG, Morgan D, Les DH, Mishler BD, Duvall MR, Price RA, Hills HG, Qiu YL, Kron KA, Rettig JH, Conti E, Palmer JD, Manhart JR, Sytsma KJ, Michaels HJ, Kress WJ, Karol KG, Clark WD, Hédren MH, Gaut BS, Jansen RK, Kim KJ, Wimpee CF, Smith JF, Furnier GR, Strauss SH, Xiang QY, Plunkett GM, Soltis PS, Swensen SM, Williams SE, Gadek PA, Quinn CJ, Equiarte LE, Dolenberg E, Learn Jr GH, Graham SW, Barrett SCH, Dayandan S, Albert VA (1993) Phylogenetics of seed plants: An analysis of nucleotide sequences from the plastid gene rbcL. Ann Mo Bot 80:528–580
Felsenstein J (2004) PHYLIP (Phylogeny Inference Package) version 3.6. Distributed by the author, Department of Genome Sciences, University of Washington, Seattle
Felsenstein J, Churchill GA (1996) A hidden Markov Model approach to variation among sites in rate of evolution. Mol Biol Evol 13:93–104
Gascuel O (1997) BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. Mol Biol Evol 14:685–695
Howe K, Bateman A, Durbin R (2002) QuickTree: Building huge neighbour-joining trees of protein sequences. Bioinformatics 18:1546–1547
Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111–120
Kishino H, Hasegawa M (1989) Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in Hominoidea. J Mol Evol 19:170–179
Kuhner MK, Felsenstein J (1994) A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates. Mol Biol Evol 11:459–468
Mailund T, Pedersen CNS (2004) QuickJoin—Fast neighbour-joining tree reconstruction. Bioinformatics 20:3261–3262
Moret BME, Nakhleh L, Warnow T, Linder CR, Tholse A, Padolina A, Sun J, Timme R (2004) Phylogenetic networks: modeling, reconstructibility, and accuracy. IEEE/ACM Trans Comput Biol Bioinform 1:13–23
Robinson DF, Foulds LR (1981) Comparison of phylogenetic trees. Math Bioscie 53:131–147
Saitou N, Imanishi T (1989) Relative efficiencies of the Fitch-Margoliash, maximum-parsimony, maximum-likelihood, minimum-evolution, and neighbor-joining methods of phylogenetic tree construction in obtaining the correct tree. Mol Biol Evol 6:514–525
Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425
Stoye J, Evers D, Meyer F (1998) Rose: generating sequence families. Bioinformatics 14:157–163
Studier JA, Keppler KJ (1988) A note on the neighbor-joining algorithm of Saitou and Nei. Mol Biol Evol 5:729–731
Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673–4680
Waterman MS, Smith TF, Singh M, Beyer WA (1977) Additive evolutionary trees. J Theor Biol 64:199–213
Acknowledgments
The authors thank Paul Joyce and Holly Wichman for their suggestions regarding experimental design, Bryan Carstens, Jack Sullivan, the students in the spring 2005 systematic biology course at the University of Idaho, and two anonymous reviewers for their review comments, and Bernard Moret for discussions regarding distance metrics. Evans and Foster were partially funded by NIH NCRR 1P20 RR16448. Sheneman was partially funded by NIH P20 RR16454 from the INBRE Program of the National Center for Research Resources. Some of the experiments were run on the IBEST Beowulf cluster, which is funded in part by NSF EPS 00809035, NIH NCRR 1P20 RR16448, and NIH NCRR 1P20 RR16454.
Author information
Authors and Affiliations
Corresponding author
Additional information
[Reviewing Editor: Dr. James Bull]
Rights and permissions
About this article
Cite this article
Evans, J., Sheneman, L. & Foster, J. Relaxed Neighbor Joining: A Fast Distance-Based Phylogenetic Tree Construction Method. J Mol Evol 62, 785–792 (2006). https://doi.org/10.1007/s00239-005-0176-2
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00239-005-0176-2