Why neighbor-joining works

Algorithmica (New York)

Volumn 54, Issue 1, 2009, Pages 1-24

  Mihaescu, Radu ^a   Levy, Dan ^a   Pachter, Lior ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Distance methods; Edge radius; Neighbor joining; Quartets

Indexed keywords

DISTANCE METHODS; EDGE RADIUS; NEIGHBOR-JOINING; NEIGHBOR-JOINING ALGORITHMS; OPTIMAL RADIUS; PERFORMANCE GUARANTEES; QUADRATIC TIME; QUARTETS; THEORETICAL BASIS;

TREES (MATHEMATICS);

JOINING;

EID: 64949116073     PISSN: 01784617     EISSN: 14320541     Source Type: Journal    
DOI: 10.1007/s00453-007-9116-4     Document Type: Article

References (30)

1. K. Atteson 1999 The performance of neighbor-joining methods of phylogenetic reconstruction Algorithmica 25 251 278
2. W.J. Bruno N.D. Socci A.L. Halpern 2000 Weighted neighbor-joining: a likelihood-based approach to distance-based phylogeny reconstruction Mol. Biol. Evol. 17 1 189 197
3. D. Bryant 2005 On the uniqueness of the selection criterion in neighbor-joining J. Classif. 22 1 3 15
4. ∞ radius of Saitou and Nei's method for phylogenetic reconstruction Theor. Comput. Sci. 369 1-3 448 455
5. Desper, R., Gascuel, O.: The minimum evolution distance-based approach to phylogenetic inference. In: Gascuel, O. (ed.) Mathematics of Evolution and Phylogeny. Oxford University Press, Oxford (2005)
6. Elias, I., Lagergren, J.: Fast neighbor joining. In: Proceedings of the International Colloquium on Automata, Languages and Programming (ICALP'05) (2005)
7. P.L. Erdös M.A. Steel L.A. Székely T.J. Warnow 1999 A few logs suffice to build (almost) all trees, I Random Struct. Algorithms 14 2 153 184
8. J.S. Farris V.A. Albert M. Källersjö D. Lipscomb A.G. Kluge 1996 Parsimony jackknifing outperforms neighbor-joining Cladistics 12 99 124
9. Felsenstein, J.: PHYLIP (phylogeny inference package) version 3.5c. Tech. report, Department of Genetics, University of Washington, Seattle (1993)
10. O. Gascuel 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 6 961 963
11. O. Gascuel 1997 BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data Mol. Biol. Evol. 14 7 685 695
12. O. Gascuel M. Steel 2006 Neighbor-joining revealed Mol. Biol. Evol. 23 11 1997 2000
13. B.G. Hall 2005 Comparison of the accuracies of several phylogenetic methods using protein and DNA sequences Mol. Biol. Evol. 22 3 792 802
14. J. Huelsenbeck D. Hillis 1993 Success of phylogenetic methods in the four-taxon case Syst. Biol. 42 3 247 264
15. K.St. John T. Warnow B. Moret L. Vawter 2003 Performance study of phylogenetic methods: (unweighted) quartet methods and neighbor joining J. Algorithms 48 174 193
16. M.K. Kuhner J. Felsenstein 1994 A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates Mol. Biol. Evol. 11 459 468
17. S. Kumar S.R. Gadagker 2000 Efficiency of the neighbor-joining method in reconstructing evolutionary relationships in large phylogenies J. Mol. Evol. 51 544 553
18. D. Levy R. Yoshida L. Pachter 2006 Beyond pairwise distances: neighbor joining with phylogenetic diversity estimates Mol. Biol. Evol. 23 491 498
19. G.J. Olsen H. Matsuda R. Hagstrom R. Overbeek 1994 fastDNAml: a tool for construction of phylogenetic trees of DNA sequences using maximum likelihood Comput. Appl. Biosci. 10 41 48
20. S. Ota W.H. Li 2000 NJML: a hybrid algorithm for the neighbor-joining and maximum likelihood methods Mol. Biol. Evol. 17 9 1401 1409
21. Y. Pauplin 2000 Direct calculation of tree length using a distance matrix J. Mol. Evol. 51 41 47
22. A. Rambaut N.C. Grassly 1997 Seq-Gen: an application for the Monte Carlo simulation of DNA sequences evolution along phylogenetic trees Comput. Appl. Biosci. 13 235 238
23. V. Ranwez O. Gascuel 2002 Improvement of distance-based phylogenetic methods by a local maximum likelihood approach using triplets Mol. Biol. Evol. 19 11 1952 1963
24. N. Saitou M. Nei 1987 The neighbor joining method: a new method for reconstructing phylogenetic trees Mol. Biol. Evol. 4 4 406 425
25. S. Sattath A. Tversky 1977 Additive similarity trees Psychometrika 42 6 319 345
26. Semple, C., Steel, M.: Phylogenetics. Graduate Series in Mathematics and its Applications. Oxford University Press, Oxford (2003)
27. K. Strimmer A. von Haeseler 1996 Quartet puzzling: a quartet maximum likelihood method for reconstructing tree topologies Mol. Biol. Evol. 13 964 969
28. J.A. Studier K.J. Keppler 1988 A note on the neighbor-joining method of Saitou and Nei Mol. Biol. Evol. 5 729 731
29. K. Tamura M. Nei S. Kumar 2004 Prospects for inferring very large phylogenies by using the neighbor-joining method Proc. Natl. Acad. Sci. 101 11030 11035
30. ∞ radius of Saitou and Nei's method for phylogenetic reconstruction Inf. Process. Lett. 94 225 230