Choosing the tree which actually best explains the data: Another look at the bootstrap in phylogenetic reconstruction

Computational Statistics and Data Analysis

Volumn 32, Issue 3-4, 2000, Pages 273-283

  Berry, V ^a   Gascuel, O ^a   Caraux, G ^a  

^a LIRMM   (France)

Author keywords

Bootstrap resampling methods; Complexity goodness of fit; Cross validation; Four point condition; Overfitting; Phylogeny reconstruction; Quartets; Structural distance; Tree estimation

Indexed keywords

COMPUTATIONAL COMPLEXITY; DATA REDUCTION; MATHEMATICAL MODELS;

BOOTSTRAP RESAMPLING METHODS; PHYLOGENETIC RECONSTRUCTION;

TREES (MATHEMATICS);

EID: 0038998792     PISSN: 01679473     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0167-9473(99)00081-X     Document Type: Article

References (28)

1. Bandelt H.-J., Dress A. Reconstructing the shape of a tree from observed dissimilarity data. Adv. Appl. Math. 7:1986;309-343.
2. Barthélemy, J., Guénoche, A., 1991. Trees and Proximities Representations. Wiley, Chichester.
3. Berry, V., 1997. Méthodes et algorithmes pour reconstruire les arbres de l'Évolution. Ph.D. Thesis, Université de Montpellier.
4. Berry V., Gascuel O. On the interpretation of bootstrap trees: appropriate threshold of clade selection and induced gain. Mol. Biol. Evol. 13(7):1996;999-1011.
5. Breiman, L., Friedman, J., Olshen, A., Stone, C.J., 1984. Classification and Regression Trees. Belmont, Wadsworth.
6. Buneman, P., 1974. A note on metric properties of trees. J. Combin. Theory 17(B), 48-50.
7. Efron B. Bootstrap methods: another look at the jackknife. Ann. Statist. 7:1979;1-26.
8. Efron, B., Halloran, E., Holmes, S., 1995. Bootstrap confidence levels for phylogenetic trees. Technical Report Tech. Rep. 179, Standford University.
9. Efron, B., Tibshirani, R.J., 1993. An Introduction to the Bootstrap. Chapman & Hall, London.
10. Felsenstein J. Confidence limites on phylogenies: an approach using the bootstrap. Evolution. 39(4):1985;783-791.
11. Fitch W.M. A non-sequential method for constructing trees and hierarchical classifications. J. Mol. Evol. 18:1981;30-37.
12. Gascuel O. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. Mol. Biol. Evolut. 14:1997;685-695.
13. Gascuel O., Levy D. A reduction for approximating a (non-metric) dissimilarity by a tree distance. J. Classification. 13:1996;129-155.
14. Hillis D.M., Bull J.J. An empirical test of bootstrapping as a method for assessing confidence in phylogenetic analysis. Systems Biol. 42:1993;192-200.
15. Jukes, T.H., Cantor, C.R., 1969. Evolution of protein molecules. In: Munro, H.N. (Ed.), Mammalian Protein Metabolism, Vol. III. Academic Press, New York, pp. 21-132 (Chapter 24).
16. Kimura M. A simple method for estimating evolutionary rates base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 16:1980;111-120.
17. Kuhner M., Felsenstein J. A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates. Mol. Biol. Evol. 11:1994;459-468.
18. Larget B., Simon D.L. Markov chain monte carlo algorithms for the Bayesian analysis of phylogenetic trees. Mol. Biol. Evol. 16(6):1999;750-759.
19. Li, W.-H., Gouy, M., 1990. Statistical tests of molecular phylogenies. In: Doolittle, R.F. (Ed.), Molecular Evolution: Computer Analysis of Protein and Nucleic acid Sequences, Methods In Enzymology, Vol. 183. Academic Press, New York, pp. 645-659 (Chapter 40).
20. Li W.-H., Zharkikh A. Statistical tests of DNA phylogenies. Systems Biol. 44:1995;49-63.
21. Robinson D.F., Foulds L.R. Comparison of phylogenetic trees. Math. Biosci. 53:1981;131-147.
22. Rzhetsky A., Kumar S., Nei M. Four-cluster analysis: a simple method to test phylogenetic hypotheses. Mol. Biol. Evol. 12(1):1995;163-167.
23. Saitou N., Nei M. The neighbor-joining method: A new method for reconstruction phylogenetic trees. Mol. Biol. Evol. 4(4):1987;406-425.
24. Sattah S., Tversky A. Additive similarity trees. Psychometrika. 42:1977;319-345.
25. Steel M. The complexity of reconstructing trees from qualitative characters and subtrees. J. Classification. 9:1992;91-116.
26. Swofford, D.L., Olsen, G.J., 1990. Phylogeny reconstruction. In: Hillis, D.M., Moritz, C. (Eds.), Molecular Systematics. Sinauer Associates, Inc., Sunderland, MA, USA, pp. 411-501 (Chapter 11).
27. Zaretskii, K., 1965. Construction of a tree on the basis of a set of distances between its leaves. Upekki Math. Nauk. 20, 90-92 (in Russian).
28. Zharkikh A., Li W.-H. Estimation of confidence in phylogeny: the complete-and-partial bootstrap technique. Mol. Phylogenet. Evol. 4(1):1995;44-63.