Moscow University Biological Sciences Bulletin

, Volume 65, Issue 4, pp 139–141 | Cite as

Comparison of protein phylogeny reconstruction methods using natural protein sequences

Article

Abstract

Comparison of several protein phylogeny reconstruction methods was realized on a set of natural protein sequences. The programs of the PHYLIP package and FastME, PhyML and TreeTop programs were tested. In contrast to several studied programs that used simulated sequences, our results demonstrate the superiority of distance methods over the maximum likelihood method.

Keywords

phylogeny reconstruction algorithms protein sequences 

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. 1.
  2. 2.
    Fitch, W.M. and Margoliash, E., Construction of Phylogenetic Trees, Science, 1967, vol. 155, pp. 406–416.CrossRefGoogle Scholar
  3. 3.
    Cavalli-Sforza, L.L. and Edwards, A.W.F., Phylogenetic Analysis: Models and Estimation Procedures, Evolution, 1967, vol. 32, pp. 550–570.CrossRefGoogle Scholar
  4. 4.
    Saitou, N. and Nei, M., The Neighbor-Joining Method: A New Methods for Reconstructing Phylogenetic Trees, Mol. Biol. Evol., 1987, vol. 4, pp. 406–425.PubMedGoogle Scholar
  5. 5.
    Sokal, R.R. and Sneath, P.H.A., Numerical Taxonomy, San Francisco: Freeman, 1963.Google Scholar
  6. 6.
    Hall, G.B., Comparison of the Accuracies of Several Phylogenetic Methods using Protein and DNA Sequences, Mol. Biol. Evol., 2005, vol. 22, pp. 792–802.CrossRefPubMedGoogle Scholar
  7. 7.
    Kuhner, K.M. and Felsenstein, J., A Simulation Comparison of Phylogeny Algorithms under Equal and Unequal Evolutionary Rates, Mol. Biol. Evol., 1994, vol. 11, pp. 459–468.PubMedGoogle Scholar
  8. 8.
    Guindon, S. and Gascuel, O., A Simple, Fast and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood, Syst. Biol., 2003, vol. 52, pp. 696–704.CrossRefPubMedGoogle Scholar
  9. 9.
    Desper, R. and Gascuel, O., Fast and Accurate Phylogeny Reconstruction Algorithms Based on Minimum-Evolution Principle, J. comput. Biol., 2002, no. 9, pp. 687–705.Google Scholar
  10. 10.
    Chumakov, K.M. and Yushmanov, S.V., Algorithms for Constructing Phylogenetic Trees of Maximum Topological Similarity, Mol. Gen. Mikrobiol. Virusol., 1988, no. 3, pp. 9–15 [in Russian].Google Scholar
  11. 11.
    Web-Interface of the TreeTop Program: (URL: http://www.genebee.msu.ru/services/phtree-reduced.html (05.04.2010).
  12. 12.
    Finn, R.D. et al., The Pfam Protein Families Database, Nucleic Acids Res., 2010 Database Issue 38, pp. D211–D222.Google Scholar
  13. 13.
    Kimura, M., The Neutral Theory of Molecular Evolution, Cambridge: Cambridge Univ. Press, 1983.CrossRefGoogle Scholar

Copyright information

© Allerton Press, Inc. 2010

Authors and Affiliations

  1. 1.Department of Bioengineering and Bioinformatics, Belozersky Institute of Physical and Chemical BiologyMoscow State UniversityMoscowRussia

Personalised recommendations