Neighbor-joining revealed

Molecular Biology and Evolution

Volumn 23, Issue 11, 2006, Pages 1997-2000

  Gascuel, Olivier ^a   Steel, Mike ^b  

^a LIRMM   (France)

^b UNIVERSITY OF CANTERBURY   (New Zealand)

Author keywords

Algorithm; Consistency; Distance method; Minimum evolution; Neighbor Joining; Phylogenetic criterion

Indexed keywords

ALGORITHM; EVOLUTION; GENETIC DISTANCE; MATHEMATICAL ANALYSIS; MEDICAL LITERATURE; NEIGHBOR JOINING METHOD; PHYLOGENETIC TREE CONSTRUCTION METHOD; RELIABILITY; REVIEW;

ALGORITHMS; CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; EVOLUTION, MOLECULAR; HUMANS; MODELS, GENETIC; PHYLOGENY;

EID: 33749540417     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msl072     Document Type: Review

References (31)

1. Atteson K. 1999. The performance of the neighbor-joining methods of phylogenetic reconstruction. Algorithmica 25:251-78.
2. Bryant D. 2005. On the uniqueness of the selection criterion in neighbor-joining. J Classif 22:3-15.
3. Desper R, Gascuel O. 2002. Fast and accurate phylogeny reconstruction algorithms based on the minimum-evolution principle. J Comput Biol 9:687-705.
4. Desper R, Gascuel O. 2004. Theoretical foundations of the balanced minimum evolution method of phylogenetic inference and its relationship to weighted least-squares tree fitting. Mol Biol Evol 21:587-98.
5. Desper R, Gascuel O. 2005. The minimum evolution distance-based approach to phylogenetic inference. In: Gascuel O, editor. Mathematics of evolution & phylogeny. Oxford, UK: Oxford University Press. p 1-32.
6. Felsenstein J. 2004. Inferring phylogenies. Sunderland, MA: Sinauer Associates.
7. Fitch WM, Margoliash E. 1967. Construction of phylogenetic trees. Science 155:279-84.
8. Gascuel O. 1994. A note on Sattath and Tversky's, Saitou and Nei's and Studier and Keppler's algorithms for inferring phylogenies from evolutionary distances. Mol Biol Evol 11:961-3.
9. Gascuel O. 1997. Concerning the NJ algorithm and its unweighted version, UNJ. In: Mirkin B, McMorris FR, Roberts FS, Rzhetsky A, editors. Mathematical hierarchies and biology. DIMACS series in discrete mathematics and theoretical computer science. Providence, RI: American Mathematical Society. p 149-70.
10. Gascuel O. 2000. On the optimization principle in phylogenetic analysis and the minimum-evolution criterion. Mol Biol Evol 17:401-5.
11. Kimura M. 1980. A simple method for estimating evolutionary rate of base substitution through comparative studies of nucleotide sequences. J Mol Evol 16:111-20.
12. Kuhner MK, Felsenstein J. 1994. A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates. Mol Biol Evol 11:459-68.
13. Kumar S. 1996. A stepwise algorithm for finding minimum evolution trees. Mol Biol Evol 13:584-93.
14. Levy D, Yoshida R, Pachter L. 2005. Beyond pairwise distances: neighbor joining with phylogenetic diversity estimates. Mol Biol Evol (Advanced access, November 9, 2005).
15. Makarenkov V, Leclerc B. 1997. Circular orders of tree metrics, and their uses for the reconstruction and fitting of phylogenetic trees. In: Mirkin B, McMorris FR, Roberts F, Rzhetsky A, editors. Mathematical hierarchies and biology. DIMACS series in discrete mathematics and theoretical computer science. Providence, RI: American Mathematical Society. p 183-208.
16. Mihaescu R, Levy D, Pachter L. 2006. Why neighbour-joining works. arXiv:cs.DS/0602041 v1.
17. Mirkin B. 1996. Mathematical classification and clustering. London: Kluwer Academic Publishers.
18. Nei M, Kumar S. 2000. Molecular evolution and phylogenetics. Oxford, UK: Oxford University Press.
19. Nei M, Kumar S, Takahashi K. 1998. The optimization principle in phylogenetic analysis tends to give incorrect topologies when the number of nucleotides or amino acids used is small. Proc Natl Acad Sci 95:12390-7.
20. Pauplin Y. 2000. Direct calculation of a tree length using a distance matrix. J Mol Evol 51:41-7.
21. Rzhetsky A, Nei M. 1993. Theoretical foundation of the minimumevolution method of phylogenetic inference. Mol Biol Evol 10:1073-95.
22. Saitou N. 1996. Reconstruction of gene trees from sequence data. In: Doolittle R, editor. Methods in enzymology. Volume 266. Orlando, FL: Academic Press, Inc. p 427-49.
23. Saitou N, Imanishi M. 1989. 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 6:514-25.
24. Saitou N, Nei M. 1987. The neighbor-joining method: a new method for reconstruction of phylogenetic trees. Mol Biol Evol 4:406-25.
25. Semple C, Steel M. 2003. Phylogenetics. Oxford, UK: Oxford University Press.
26. Semple C, Steel M. 2004. Cyclic permutations and evolutionary trees. Adv Appl Math 32:669-80.
27. Studier JA, Keppler KJ. 1998. A note on the neighbor-joining method of Saitou and Nei. Mol Biol Evol 5:729-31.
28. Sumiyama K, Kim CB, Ruddle FH. 2001. An efficient cis-element discovery method using multiple sequence comparisons based on evolutionary relationships. Genomics 71:260-2.
29. Swofford DL, Olsen GL, Waddell PJ, Hillis DM. 1996. Phylogenetic inference. In: Hillis DM, Moritz C, Mable BK, editors. Molecular sytematics. Sunderland, MA: Sinauer. p 407-514.
30. Vinh LS, von Haeseler A. 2005. Shortest triplet clustering: reconstructing large phylogenies using representative sets. BMC Bioinformatics 6:92.
31. Yushmanov SV. 1984. Construction of a tree with p leaves from 2p-3 elements of its distance matrix (Russian). Matematicheskie Zametki 35:877-87.