Fast and accurate phylogeny reconstruction algorithms based on the minimum-evolution principle

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Volumn 2452, Issue , 2002, Pages 357-374

  Desper, Richard ^a   Gascuel, Olivier ^b  

^a NATIONAL INSTITUTES OF HEALTH   (United States)

^b LIRMM   (France)

Author keywords

[No Author keywords available]

Indexed keywords

BIOINFORMATICS; BIOLOGY; NEAREST NEIGHBOR SEARCH; TOPOLOGY; TREES (MATHEMATICS);

CONSTRUCTION ALGORITHMS; MINIMUM EVOLUTION PRINCIPLE; NEAREST NEIGHBORS; ORDINARY LEAST SQUARES; PHYLOGENETIC TREES; PHYLOGENY RECONSTRUCTION; RELATED ALGORITHMS; SWAPPING ALGORITHMS;

EVOLUTIONARY ALGORITHMS;

EID: 84957039932     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/3-540-45784-4_27     Document Type: Conference Paper

References (30)

1. Aldous, D.J.: Stochastic models and descriptive statistics for phylogenetic trees from Yule to today. Statist. Sci. 16 (2001) 23-34
2. Bruno, W.J., Socci, N.D., Halpern, A.L.: Weighted neighbor joining: A likelihoodbased approach to distance-based phylogeny reconstruction. Mol. Biol. Evol. 17 (2000) 189-197
3. Bryant, D., Waddell, P.: Rapid evaluation of least-squares and minimum-evolution criteria on phylogenetic trees. Mol. Biol. Evol. 15 (1998) 1346-1359
4. Bulmer, M.: Use of the method of generalized least squares in reconstructing phylogenies from sequence data. Mol. Biol. Evol. 8 (1991) 868-883
5. Cormen, T.H., Leiserson, C.E., Rivest, R.L.: Introduction to algorithms. MIT Press, Cambridge, MA (2000)
6. Csűròs, M.: Fast recovery of evolutionary trees with thousands of nodes. Journal of Computational Biology 9 (2002) 277-297
7. Denis, F., Gascuel, O.: On the consistency of the minimum evolution principle of phylogenetic inference. Discr. Appl. Math. In press (2002)
8. Erdös, P.L., Steel, M., Székély, L., Warnow, T.: A few logs suffice to build (almost) all trees: Part II. Theo. Comp. Sci. 221 (1999) 77-118
9. Felsenstein, J.: An alternating least-squares approach to inferring phylogenies from pairwise distances. Syst. Biol. 46 (1997) 101-111
10. Felsenstein, J.: PHYLIP — Phylogeny Inference Package (Version 3.2). Cladistics 5 (1989) 164-166
11. Fitch, W.M., Margoliash, E.: Construction of phylogenetic trees. Science 155 (1967) 279-284
12. 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
13. Gascuel, O.: On the optimization principle in phylogenetic analysis and the minimum-evolution criterion. Mol. Biol. Evol. 17 (2000) 401-405
14. Gascuel, O., Bryant, D., Denis, F.: Strengths and limitations of the minimum evolution principle. Syst. Biol. 50 (2001) 621-627
15. Harding, E.: The probabilities of rooted tree-shapes generated by random bifurcation. Adv. Appl. Probab. 3 (1971) 44-77
16. Kimura, M.: A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 16 (1980) 111-120
17. Kuhner, M.K., Felsenstein, J.: A simulation comparison of phylogeny algorithms under equal and unequal rates. Mol. Biol. Evol. 11 (1994) 459-468
18. McKenzie, A., Steel, M.: Distributions of cherries for two models of trees. Math. Biosci. 164 (2000) 81-92
19. Nei, M., Jin, L.: Variances of the average numbers of nucleotide substitutions within and between populations. Mol. Biol. Evol. 6 (1989) 290-300
20. Pauplin, Y.: Direct calculation of a tree length using a distance matrix. J. Mol. Evol. 51 (2000) 41-47
21. Rambaut, A., Grassly, N.C.: Seq-Gen: An application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. Computer Applications in the Biosciences 13 (1997) 235-238
22. Robinson, D., Foulds, L.: Comparison of phylogenetic trees. Math. Biosci. 53 (1981) 131-147
23. Rzhetsky, A., Nei, M.: A simple method for estimating and testing minimumevolution trees. Mol. Biol. Evol. 9 (1992) 945-967
24. Rzhetsky, A., Nei, M.: Theoretical foundation of the minimum-evolution method of phylogenetic inference. Mol. Biol. Evol. 10 (1993) 1073-1095
25. Saitou, N., Nei, M.: The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4 (1987) 406-425
26. Sneath, P.H.A., Sokal, R.R. In: Numerical Taxonomy. W.K. Freeman and Company, San Francisco (1973) 230-234
27. Swofford, D.: PAUP—Phylogenetic Analysis Using Parsimony (and other methods), Version 4.0 (1996)
28. Swofford, D.L., Olsen, G.J., Waddell, P.J., Hillis, D.M.: Phylogenetic inference. In Hillis, D., Moritz, C., Mable, B., eds.: Molecular Systematics. Sinauer, Sunderland, MA (1996) 407-514
29. Vach, W.: Least squares approximation of addititve trees. In Opitz, O., ed.: Conceptual and numerical analysis of data. Springer-Verlag, Berlin (1989) 230-238
30. Yule, G.: A mathematical theory of evolution, based on the conclusions of Dr. J. C. Willis. Philos. Trans. Roy. Soc. London Ser. B, Biological Sciences 213 (1925) 21-87