Efficient and robust analysis of large phylogenetic datasets

Advanced Data Mining Technologies in Bioinformatics

Volumn , Issue , 2006, Pages 104-117

  Rahmann, Sven ^a   Müller, Tobias ^b   Dandekar, Thomas ^b   Wolf, Matthias ^b  

^a BIELEFELD UNIVERSITY   (Germany)

^b UNIVERSITY OF WÜRZBURG   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84900226404     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.4018/978-1-59140-863-5.ch006     Document Type: Chapter

References (33)

1. Barry, D., & Hartigan, J. (1987). Asynchronous distance between homologous DNA sequences. Biometrics, 43, 261-276.
2. Bininda-Emonds, O. R. P. (2004). The evolution of supertrees. Trends in Ecology and Evolution, 19(6), 315-322.
3. Bruno, W. J., Socci, N. D., & Halpern, A. L. (2000). Weighted neighbor joining: A likelihood-based approach to distance-based phylogeny reconstruction. Molecular Biology and Evolution, 17, 189-197.
4. Camin, J., & Sokal, R. (1965). A method for deducing branching sequences in phylogeny. Evolution, 19, 311-326.
5. Desper, R., & Gascuel, O. (2002). Fast and accurate phylogeny reconstruction algorithms based on the minimum-evolution principle. Journal of Computational Biology, 19, 687-705.
6. Efron, B., Halloran, E., & Holmes, S. (1996). Bootstrap confidence levels for phylogenetic trees. PNAS, 93, 7085-7090.
7. Ewens, W. J., & Grant, G. R. (2001). Statistical Methods in Bioinformatics. New York: Springer-Verlag
8. Felsenstein, J. (1981). Evolutionary trees from DNA sequences: A maximum likelihood approach. Journal of Molecular Evolution, 17, 368-376.
9. Felsenstein, J. (1985). Confidence limits on phylogenies: An approach using the bootstrap. Evolution, 39, 783-791.
10. Felsenstein, J. (2003). Inferring Phylogenies. Sunderland, MA: Sinauer Associates.
11. Fitch, W.M. (1971). Toward defining the course of evolution: Minimum change for a specified tree topology. Systematic Zoology, 20, 406-416
12. Friedrich, J., Wolf, M., Dandekar, T., & Müller, T. (2005): ProfDist: A tool for the construction of large phylogenetic trees based on profile distances. Bioinformatics, 21, 2108-2109.
13. Gascuel, O. (1997). BIONJ: An improved version of the NJ algorithm based on a simple model of sequence data. Molecular Biology and Evolution, 14, 685-695.
14. Gribskov, M., McLachlan, A., & Eisenberg, D. (1987). Profile analysis: Detection of distantly related proteins. PNAS, 84, 4355-4358.
15. Hillis, D., & Bull, J. (1993). An empirical test of bootstrapping as a method for assessing confidence in phylogenetic analysis. Systematic Biology, 42, 182-192.
16. Holder, M., & Lewis, P. (2003). Phylogeny estimation: Traditional and Bayesian approaches. Nature Reviews, 4, 275-284.
17. Huelsenbeck, J., & Ronquist, F. (2001). MRBAYES: Bayesian inference of phylogeny. Bioinformatics, 17, 754-755.
18. Huson, D. H., Nettles, S. M., & Warnow, T. J. (1999). Disk-covering, a fast-converging method for phylogenetic tree reconstruction. Journal of Computational Biology, 6, 369-386.
19. Jukes, T., & Cantor, C. R. (1969). Evolution of protein molecules. In H. Munro (Ed.), Mammalian protein metabolism (pp. 21-132). New York: Academic Press.
20. Kimura, M. (1980). A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. Journal of Molecular Evolution, 16, 111-120.
21. Krogh, A., & Mitchison, G. (1995). Maximum entropy weighting of aligned sequences of proteins or DNA. In C. Rawlings, D. Clark, R. Altman, L. Hunter, T. Lengauer, & S. Wodak (Eds.), Proceedings of the Third International Conference on Intelligent Systems for Molecular Biology (pp. 215-221). Menlo Park, CA: AAAI Press.
22. Lanave, C., Preparata, G., Saccone, C., & Serio, G. (1984). A new method for calculating evolutionary substitution rates. Journal of Molecular Evolution, 20, 86-93.
23. Müller, T., Rahmann, S., Dandekar, T., & Wolf, M. (2004). Accurate and robust phylogeny estimation based on profile distances: a study of the Chlorophyceae (Chlorophyta). BMC Evolutionary Biology, 4(20).
24. Müller, T., & Vingron, M. (2000). Modeling amino acid replacement. Journal of Computational Biology, 7, 761-776.
25. Page, R. D. M. (1996). TREEVIEW: An application to display phylogenetic trees on personal computers. Computer Applications in the Biosciences, 12, 357-358.
26. Robinson, D., & Foulds, L. (1981). Comparison of phylogenetic trees. Mathematical Biosciences, 53, 131-147.
27. Saitou, N., & Nei, M. (1987). The neighbor-joining method: A new method for reconstructing phylogenetic trees. Journal of Molecular Evolution, 4, 406-425.
28. Schmidt, H. A., & von Haeseler, A. (2003). Maximum-likelihood analysis using TREEPUZZLE. In A. D. Baxevanis, D. B. Davison, R. D. M. Page, G. Stormo, & L. Stein (Eds.), Current protocols in bioinformatics (Unit 6.6). New York: Wiley and Sons.
29. Steel, M., & Hein, J. (2001). Applying the Thorne-Kishino-Felsenstein model to sequence evolution on a star-shaped tree. Applied Mathematics Letters, 14, 679-684.
30. Swofford, D. L. (2003). PAUP*: Phylogenetic Analysis Using Parsimony (*and other methods), Version 4. Sunderland, MA: Sinauer Associates.
31. van de Peer, Y., Baldauf, S. L., Doolittle, W. F., & Meyer, A. (2000). An updated and comprehensive rRNA phylogeny of (crown) eukaryotes based on rate-calibrated evolutionary distances. Journal of Molecular Evolution, 51, 565-76.
32. Wuyts, J., Perriere, G., & Van de Peer, Y. (2004). The European ribosomal RNA database. Nucleic Acids Research, 32, 101-103. Retrieved February, 2006, from http://www.psb.ugent.be/rRNA
33. Zmasek, C., & Eddy, S. (2001). ATV: display and manipulation of annotated phylogenetic trees. Bioinformatics, 17, 383-384.