The tree nearest on average to a given set of trees

Large Systems

Abstract

We formulate the problem of constructing a tree which is the nearest on average to a given set of trees. The notion of “nearest” is formulated based on a conception of events such that counting their number makes it possible to distinguish each of the given trees from the desired one. These events are called divergence, duplication, loss, and transfer; other lists of events can also be considered. We propose an algorithm that solves this problem in cubic time with respect to the input data size. We prove correctness of the algorithm and a cubic estimate for its complexity.

References

  1. 1.
    Phylogenetic Supertrees. Combining Information to Reveal the Tree of Life, Bininda-Emonds, O.R.P., Ed., Dordrecht: Kluwer, 2004.MATHGoogle Scholar
  2. 2.
    Guigo, R., Muchnik, I., and Smith, T.F., Reconstruction of Ancient Molecular Phylogeny, Mol. Phylogenet. Evol., 1996, vol. 6, no. 2, pp. 189–213.CrossRefGoogle Scholar
  3. 3.
    Gorbunov, K.Yu. and Lyubetsky, V.A., Reconstructing the Evolution of Genes along the Species Tree, Molekulyarnaya Biol., 2009, vol. 43, no. 5, pp. 946–958 [Molecular Biol. (Engl. Transl.), 2009, vol. 43, no. 5, pp. 881–893].Google Scholar
  4. 4.
    Gorbunov, K.Yu. and Lyubetsky, V.A., On An Algorithm for Gene/Species Trees Reconciliation Taking into Account Duplications, Losses, and Horizontal Gene Transfers, Inform. Protsessy, 2010, vol. 10, no. 2, pp. 140–144.Google Scholar
  5. 5.
    Gorbunov, K.Yu. and Lyubetsky, V.A., Fast Algorithm for Building Species Supertrees Given a Set of Protein Trees, to appear in Molekulyarnaya Biol., 2011.Google Scholar
  6. 6.
    Gorbunov, K.Yu. and Lyubetsky, V.A., Identification of Ancestral Genes That Introduce Incongruence between Protein- and Species Trees, Molekulyarnaya Biol., 2005, vol. 39, no. 5, pp. 847–858 [Molecular Biol. (Engl. Transl.), 2005, vol. 39, no. 5, pp. 741–751].Google Scholar
  7. 7.
    Doyon, J.P., Scornavacca, C., Gorbunov, K.Yu., Szeollosi, G.J., Ranwez, V., and Berry, V., An Efficient Algorithm for Gene/Species Trees Parsimonious Reconciliation with Losses, Duplications and Transfers, Comparative Genomics (Proc. Int. Workshop RECOMB-CG 2010, Ottawa, Canada, 2010), Tannier, E., Ed., Lect. Notes Comp. Sci., vol. 6398, Lecture Notes in Bioinformatics, Berlin: Springer, 2010, pp. 93–108.Google Scholar

Copyright information

© Pleiades Publishing, Ltd. 2011

Authors and Affiliations

  1. 1.Kharkevich Institute for Information Transmission ProblemsRussian Academy of SciencesMoscowRussia

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