Random local neighbor joining: A new method for reconstructing phylogenetic trees

Molecular Phylogenetics and Evolution

Volumn 47, Issue 1, 2008, Pages 117-128

  Zhang, Wei ^a   Sun, Zhirong ^a  

^a Tsinghua University   (China)

Author keywords

Minimum evolution; Neighbor joining; Phylogenetic reconstruction; Random local neighbor joining; Reliability

Indexed keywords

ALGORITHM; ARTICLE; PHYLOGENY;

ALGORITHMS; PHYLOGENY;

EID: 41149168522     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2008.01.019     Document Type: Article

References (41)

1. Alfaro M.E., Zoller S., and Lutzoni F. Bayes or bootstrap? A simulation study comparing the performance of Bayesian Markov Chain Monte Carlo sampling and bootstrapping in assessing phylogenetic confidence. Mol. Biol. Evol. 20 (2003) 255-266
2. Bandelt H.J., and Dress A. Split decomposition: a new and useful approach to phylogenetic analysis of distance data. Mol. Phylogenet. Evol. 1 (1992) 242-252
3. Bruno W.J., Socci N.D., and Halpern A.L. Weighted neighbor joining: a likelihood-based approach to distance-based phylogeny reconstruction. Mol. Biol. Evol. 17 (2000) 189-197
4. Charleston M.A., Hendy M.D., and Penny D. Neighbor-joining uses the optimal weight for net divergence. Mol. Phylogenet. Evol. 2 (1993) 6-12
5. Day W. Computational complexity of inferring phylogenies from dissimilarity matrices. Bull. Math. Biol. 49 (1987) 461-467
6. Douady C.J., Delsuc F., Boucher Y., Doolittle W.F., and Douzery E.J.P. Comparison of Bayesian and maximum likelihood bootstrap measures of phylogenetic reliability. Mol. Biol. Evol. 20 (2003) 248-254
7. Efron B. Bootstrap methods: another look at the jackknife. Ann. Stat. 7 (1979) 1-26
8. Efron B., Halloran E., and Holmes S. Bootstrap confidence levels for phylogenetic trees. Proc. Natl. Acad. Sci. USA 93 (1996) 7085-7090
9. Elias, I., Lagergren, J. 2005. Fast neighbor joining. ICALP 2005, LNCS 3580, pp. 1263-1274.
10. Felsenstein J. Numerical methods for inferring evolutionary trees. Q. Rev. Biol. 57 (1982) 379-404
11. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39 (1985) 783-791
12. Felsenstein J. Phylogenies from molecular sequences: inference and reliability. Annu. Rev. Genet. 22 (1988) 521-565
13. Felsenstein J., and Kishino H. Is there something wrong with the bootstrap on phylogenies? A reply to Hillis and Bull. Syst. Biol. 42 (1993) 193-200
14. Fitch W.M., and Margoliash E. Construction of phylogenetic trees. Science 155 (1967) 279-284
15. Fitch W.M. Toward defining the course of evolution: minimum change for a specific tree topology. Syst. Zool. 20 (1971) 406-416
16. Foulds L.R., and Graham R.L. The steiner problem in phylogeny is NP-complete. Adv. Appl. Math. 3 (1982) 43-49
17. Gascuel O. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. Mol. Biol. Evol. 14 (1997) 685-695
18. Gascuel O. Concerning the NJ algorithm and its unweighted version, UNJ. In: Mirkin B., McMorris F.R., and Rzetsky A. (Eds). Mathematical Hierarchies and Biology (1997), American Mathematical Society, Providence 149-170
19. Goldman N., Anderson J.P., and Rodrigo A.G. Likelihood based tests of topologies in phylogenetics. Syst. Biol. 49 (2000) 652-670
20. Hartigan J.A. Minimum mutation fits to a given tree. Biometrics 29 (1973) 53-65
21. Hasegawa M., and Fujiwara M. Relative efficiencies of the maximum likelihood, maximum parsimony, and neighbor-joining methods for estimating protein phylogeny. Mol. Phylogenet. Evol. 2 (1993) 1-5
22. Hillis D.M., and Bull J.J. An empirical test of bootstrapping as a method for assessing confidence in phylogenetic analysis. Syst. Biol. 42 (1993) 182-192
23. Huelsenbeck J.P. The performance of phylogenetic methods in the four-taxon case. Syst. Biol. 44 (1995) 17-48
24. Kuhner M.K., and Felsenstein J. A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates. Mol. Biol. Evol. 11 (1994) 459-468
25. Kumar S. A stepwise algorithm for finding minimum evolution trees. Mol. Biol. Evol. 13 (1996) 584-593
26. Nei, M., Kumar, S. 2000. Molecular Evolution and Phylogenetics. Oxford University Press, New York. Chinese translation by Lv BZ, Zhong, Y., Gao, L.P., et al., 2002. High Education Press, Beijing.
27. Ota S., and Li W.H. NJML: a hybrid algorithm for the neighbor-joining and maximum-likelihood methods. Mol. Biol. Evol. 17 (2000) 1401-1409
28. Pearson W.R., Robins G., and Zhang T. Generalized neighbor joining: more reliable phylogenetic tree reconstruction. Mol. Biol. Evol. 16 (1999) 806-816
29. Rzhetsky A., and Nei M. A simple method for estimating and testing minimum evolution trees. Mol. Biol. Evol. 9 (1992) 945-967
30. Rzhetsky A., and Nei M. Theoretical foundation of the minimum evolution method of phylogenetic inference. Mol. Biol. Evol. 10 (1993) 1073-1095
31. Saitou N., and Imanishi M. Relative efficiencies of the Fitch-Margoliash, maximum parsimony, maximum likelihood, minimum evolution, and neighbor joining methods of phylogenetic reconstructions in obtaining the correct tree. Mol. Biol. Evol. 6 (1989) 514-525
32. Saitou N., and Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4 (1987) 406-421
33. Shi X., Gu H., Susko E., and Field C. The comparison of the confidence regions in phylogeny. Mol. Biol. Evol. 22 (2005) 2285-2296
34. Shimodaira H. An approximately unbiased test of phylogenetic tree selection. Syst. Biol. 51 (2002) 492-508
35. Sitnikova T., Rzhetsky A., and Nei M. Interior-branch and bootstrap tests of phylogenetic trees. Mol. Biol. Evol. 12 (1995) 319-333
36. Strimmer K., and Rambaut A. Inferring confidence sets of possibly misspecified gene trees. Proc. R. Soc. Lond. B 269 (2001) 137-142
37. Studier J.A., and Keppler K.J. A note on the neighbor-joining algorithm of Saitou and Nei. Mol. Biol. Evol. 5 (1988) 729-731
38. Swofford, D.L., 1996. PAUP: Phylogenetic Analysis Using Parsimony (and Other Methods), version 4.0 (test version). Sinauer Associates, Inc., Sunderland, MA.
39. Zharkikh A., and Li W.H. Statistical properties of bootstrap estimation of phylogenetic variability from nucleotide sequences: I. Four taxa with a molecular clock. Mol. Biol. Evol. 9 (1992) 1119-l147
40. Zharkikh A., and Li W.H. Statistical properties of bootstrap estimation of phylogenetic variability from nucleotide sequences: II. Four taxa without a molecular clock. J. Mol. Evol. 35 (1992) 356-366
41. Zharkikh A., and Li W.H. Estimation of confidence in phylogeny: the complete-and-partial bootstrap technique. Mol. Phylogenet. Evol. 4 (1995) 44-63