Comparison of protein phylogeny reconstruction methods using natural protein sequences
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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.
Keywordsphylogeny reconstruction algorithms protein sequences
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- 1.Site PHYLIP (URL: http://evolution.genetics.washington.edu/phylip.html 05.04.2010).
- 5.Sokal, R.R. and Sneath, P.H.A., Numerical Taxonomy, San Francisco: Freeman, 1963.Google Scholar
- 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.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.Web-Interface of the TreeTop Program: (URL: http://www.genebee.msu.ru/services/phtree-reduced.html (05.04.2010).
- 12.Finn, R.D. et al., The Pfam Protein Families Database, Nucleic Acids Res., 2010 Database Issue 38, pp. D211–D222.Google Scholar