The performance of neighbor-joining methods of phylogenetic reconstruction

Algorithmica (New York)

Volumn 25, Issue 2-3, 1999, Pages 251-278

  Atteson, K ^a  

^a YALE UNIVERSITY   (United States)

Author keywords

Evolutionary trees; Neighbor joining; Phylogenetic reconstruction

Indexed keywords

EID: 0001656793     PISSN: 01784617     EISSN: None     Source Type: Journal    
DOI: 10.1007/PL00008277     Document Type: Article

References (18)

1. R. Agarwala, V. Bafna, M. Farach, B. O. Narayanan, M. Paterson, and M. Thomp. On the approximability of numerical taxonomy. In Proceedings of the Seventh Annual ACM-SIAM Symposium on Discrete Algorithms, pages 365-372, 1996.
2. H.-J. Bandelt and A. Dress. Reconstructing the shape of a tree from observed dissimilarity data. Advances in Applied Mathematics, 7:309-343, 1986.
3. V. Berry. Méthodes et Algorithmes pour reconstruire les arbres de l'Évolution. Ph.D. thesis, Université de Montpellier, 1997.
4. J.-P. Barthélémy and A. Guénoche. Trees and Proximity Representations. Wiley, New York, 1991.
5. B. Bollobás. Graph Theory. Springer-Verlag, New York, 1979.
6. P. Buneman. The recovery of trees from measures of dissimilarity. In Mathematics in the Archeological and Historical Sciences (F. R. Hodson, D. G. Kendall, and P. Tautu, eds.). Edinburgh University Press, Edinburgh, 1971.
7. J. A. Cavender. Taxonomy with confidence. Mathematical Biosciences, 40:271-280, 1978.
8. P. L. Erdós, M. A. Steel, L. A. Székely, and T. J. Warnow. A few logs suffice to build (almost) all trees (ii). Technical Report 97-72, DIMACS, 1997.
9. J. S. Farris. A probability model for inferring evolutionary trees. Systematic Zoology, 22:250-256, 1973.
10. M. Farach and S. Kannan. Efficient algorithms for inverting evolution. In Proceedings of the Twenty-Eighth Annual ACM Symposium on the Theory of Computing, pages 230-235, 1996.
11. O. Gascuel. A note on Sattah and Tversky's, Saitou and Nei's, and Studier and Keppler's algorithms for inferring phylogenies from evolutionary distances. Molecular Biology and Evolution, 11(6):961-963, 1994.
12. O. Gascuel. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. Molecular Biology and Evolution, 14(7):685-695, 1997.
13. O. Gascuel. Concerning the NJ algorithm and its unweighted version, UNJ. In Mathematical Hierarchies and Biology, pages 149-170, American Mathematical Society, Providence, RI, 1997.
14. G. R. Grimmett and D. R. Stirzaker. Probability and Random Processes. Oxford University Press, Oxford, 1992.
15. S. Köhler, C. F. Delwiche, P. W. Denny, L. G. Tilney, P. Webster, R. J. M. Wilson, J. D. Palmer, and D. S. Roos. A plastid of probable green algal origin in apicomplexan parasites. Science, 275:1485-1489, 1997.
16. J. A. Studier and K. J. Keppler. A note on the neighbor-joining algorithm of Saitou and Nei. Molecular Biology and Evolution, 5(6):729-731, 1988.
17. N. Saitou and M. Nei. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Molecular Biology and Evolution, 4:406-425, 1987.
18. S. Sattath and A. Tversky. Additive similarity trees. Psychometrika, 42(3):319-345, 1977.