Fast and accurate phylogeny reconstruction algorithms based on the Minimum-Evolution principle

Journal of Computational Biology

Volumn 9, Issue 5, 2002, Pages 687-705

  Desper, Richard ^a   Gascuel, Olivier ^b  

^a NATIONAL INSTITUTES OF HEALTH   (United States)

^b LIRMM   (France)

Author keywords

Computational speed; Distance methods; Minimum evolution; Phylogenetic inference; Topological accuracy

Indexed keywords

ALGORITHM; ARTICLE; ASSAY; EVOLUTION; PHYLOGENETIC TREE; PHYLOGENY; PRIORITY JOURNAL; REGRESSION ANALYSIS;

ALGORITHMS; COMPUTER SIMULATION; EVOLUTION, MOLECULAR; MODELS, GENETIC; PHYLOGENY;

EID: 0036943052     PISSN: 10665277     EISSN: None     Source Type: Journal    
DOI: 10.1089/106652702761034136     Document Type: Article

References (33)

1. Aldous, D.J. 2001. Stochastic models and descriptive statistics for phylogenetic trees from Yule to today. Statist. Sci. 16, 23-34.
2. Bruno, W.J., Socci, N.D., and Halpern, A.L. 2000. Weighted neighbor joining: A likelihood-based approach to distance-based phylogeny reconstruction. Mol. Biol. Evol. 17, 189-197.
3. Bryant, D., and Waddell, P. 1998. Rapid evaluation of least-squares and minimum-evolution criteria on phylogenetic trees. Mol. Biol. Evol. 15, 1346-1359.
4. Bulmer, M. 1991. Use of the method of generalized least squares in reconstructing phylogenies from sequence data. Mol. Biol. Evol. 8, 868-883.
5. Cormen, T.H., Leiserson, C.E., and Rivest, R.L. 2000. Introduction to Algorithms, MIT Press, Cambridge, MA.
6. Csurös, M. 2002. Fast recovery of evolutionary trees with thousands of nodes. J. Comp. Biol. 9, 277-297.
7. Denis, F., and Gascuel, O. 2002. On the consistency of the minimum evolution principle of phylogenetic inference. Discr. Appl. Math. In press.
8. Erdös, P.L., Steel, M., Székély, L., and Warnow, T. 1999. A few logs suffice to build (almost) all trees: Part II. Theo. Comp. Sci. 221, 77-118.
9. Felsenstein, J. 1989. PHYLIP - Phylogeny Inference Package (Version 3.2). Cladistics 5, 164-166.
10. Felsenstein, J. 1997. An alternating least-squares approach to inferring phylogenies from pairwise distances. Syst. Biol. 46, 101-111.
11. Fitch, W.M., and Margoliash, E. 1967. Construction of phylogenetic trees. Science 155, 279-284.
12. Gascuel, O. 1997a. BIONJ: An improved version of the NJ algorithm based on a simple model of sequence data. Mol. Biol. Evol. 14, 685-695.
13. Gascuel, O. 1997b. Concerning the NJ algorithm and its unweighted version, UNJ. In Mirkin, B., McMorris, F., Roberts, F., and Rzetsky, A., eds. Mathematical Hierarchies and Biology, American Mathematical Society, Providence, RI.
14. Gascuel, O. 2000. On the optimization principle in phylogenetic analysis and the minimum-evolution criterion. Mol. Biol. Evol. 17, 401-405.
15. Gascuel, O., Bryant, D., and Denis, F. 2001. Strengths and limitations of the minimum evolution principle. Syst. Biol. 50, 621-627.
16. Guindon, S., and Gascuel, O. 2002. Efficient biased estimation of evolutionary distances when substitution rates vary across sites. Mol. Biol. Evol. 19, 534-543.
17. Harding, E. 1971. The probabilities of rooted tree-shapes generated by random bifurcation. Adv. Appl. Probab. 3, 44-77.
18. Kidd, K., and Sgaramella-Zonta, L. 1971. Phylogenetic analysis: Concepts and methods. Am. J. Human Genet. 23, 235-252.
19. 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.
20. Kuhner, M.K., and Felsenstein, J. 1994. A simulation comparison of phylogeny algorithms under equal and unequal rates. Mol. Biol. Evol. 11,459-468.
21. McKenzie, A., and Steel, M. 2000. Distributions of cherries for two models of trees. Math. Biosci. 164, 81-92.
22. Nei, M., and Jin, L. 1989. Variances of the average numbers of nucleotide substitutions within and between populations. Mol. Biol. Evol. 6, 290-300.
23. Pauplin, Y. 2000. Direct calculation of a tree length using a distance matrix. J. Mol. Evol. 51, 41-47.
24. Rambaut, A., and Grassly, N.C. 1997. Seq-Gen: An application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. Comput. Appl. Biosci. 13, 235-238.
25. Robinson, D., and Foulds, L. 1981. Comparison of phylogenetic trees. Math. Biosci. 53, 131-147.
26. Rzhetsky, A., and Nei, M. 1993. Theoretical foundation of the minimum-evolution method of phylogenetic inference. Mol. Biol. Evol. 10, 1073-1095.
27. Saitou, N., and Nei, M. 1987. The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4, 406-425.
28. Sneath, P.H.A., and Sokal, R.R. 1973. Numerical Taxonomy, 230-234, W.K. Freeman, San Francisco.
29. Swofford, D. 1996. PAUP - Phylogenetic Analysis Using Parsimony (and Other Methods), Version 4.0.
30. Swofford, D.L., Olsen, G.J., Waddell, P.J., and Hillis, D.M. 1996. Phylogenetic inference. In Hillis, D., Moritz, C., and Mable, B., eds., Molecular Systematics, 470-514, Sinauer, Sunderland, MA.
31. Tarjan, R.E. 1983. Data Structures and Network Algorithms, SIAM, Philadelphia.
32. Vach, W. 1989. Least squares approximation of addititve trees. In Opitz, O., ed. Conceptual and Numerical Analysis of Data, Springer-Verlag, Berlin.
33. Yule, G. 1925. A mathematical theory of evolution, based on the conclusions of Dr. J.C. Willis. Philos. Trans. Roy. Soc. London Ser. B, Biological Sciences 213, 21-87.