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Algorithms for Exploring the Space of Gene Tree/Species Tree Reconciliations

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Comparative Genomics (RECOMB-CG 2008)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 5267))

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Abstract

We describe algorithms to explore the space of all possible reconciliations between a gene tree and a species tree. We propose an algorithm for generating a random reconciliation, and combinatorial operators and algorithms to explore the space of all possible reconciliations between a gene tree and a species tree in optimal time. We apply these algorithms to simulated data.

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References

  1. Arvestad, L., Berglund, A.-C., Lagergren, J., Sennblad, B.: Gene tree reconstruction and orthology analysis based on an integrated model for duplications and sequence evolution. In: RECOMB 2004, pp. 326–335 (2004)

    Google Scholar 

  2. Bonizzoni, P., Della Vedova, G., Dondi, R.: Reconciling a gene tree to a species tree under the duplication cost model. Theoret. Comput. Sci. 347, 36–53 (2005)

    Article  MATH  MathSciNet  Google Scholar 

  3. Chang, W.-C., Eulenstein, O.: Reconciling gene trees with apparent polytomies. In: Chen, D.Z., Lee, D.T. (eds.) COCOON 2006. LNCS, vol. 4112, pp. 235–244. Springer, Heidelberg (2006)

    Chapter  Google Scholar 

  4. Chauve, C., Doyon, J.-P., El-Mabrouk, N.: Gene family evolution by duplication, speciation and loss. J. Comput. Biol. (to appear, 2008)

    Google Scholar 

  5. Denise, A., Zimmermann, P.: Uniform random generation of decomposable structures using floating-point arithmetic. Theoret. Comput. Sci. 218, 233–248 (1999)

    Article  MATH  MathSciNet  Google Scholar 

  6. Doyon, J.-P., Chauve, C., Hamel, S.: Algorithms for exploring the space of gene tree/species tree reconciliations. IRO Technical Report # 1323 (2008)

    Google Scholar 

  7. Fellows, M.R., Hallett, M.T., Stege, U.: On the multiple gene duplication problem. In: Chwa, K.-Y., H. Ibarra, O. (eds.) ISAAC 1998. LNCS, vol. 1533, pp. 347–356. Springer, Heidelberg (1998)

    Chapter  Google Scholar 

  8. Fitch, W.M.: Distinguishing homologous from analogous proteins. Syst. Zool. 19, 99–113 (1970)

    Article  Google Scholar 

  9. Fitch, W.M.: Homology - a personal view on some of the problems. Trends Genet. 16, 227–231 (2000)

    Article  Google Scholar 

  10. Goodman, M., Czelusniak, J., Moore, G.W., Herrera, R.A., Matsuda, G.: Fitting the gene lineage into its species lineage, a parsimony strategy illustrated by cladograms constructed from globin sequences. Syst. Zool. 28, 132–163 (1979)

    Article  Google Scholar 

  11. Górecki, P., Tiuryn, J.: DLS-trees: a model of evolutionary scenarios. Theoret. Comput. Sci. 359, 378–399 (2006)

    Article  MATH  MathSciNet  Google Scholar 

  12. Graur, D., Li, W.-H.: Fundamentals of Molecular Evolution, 2nd edn. Sinauer Associates, Sunderland (1999)

    Google Scholar 

  13. Hahn, M.W., Han, M.V., Han, S.-G.: Gene family evolution across 12 Drosophilia genomes. PLoS Genet. 3, e197 (2007)

    Article  Google Scholar 

  14. Jensen, R.: Orthologs and paralogs - we need to get it right. In: Genome Biology, 2:interactions1002.1–interactions1002.3 (2001)

    Google Scholar 

  15. Ma, B., Li, M., Zhang, L.: From gene trees to species trees. SIAM J. Comput. 30, 729–752 (2001)

    Article  MathSciNet  Google Scholar 

  16. Ma, J., Ratan, A., Zhang, L., Miller, W., Haussler, D.: A heuristic algorithm for reconstructing ancestral gene orders with duplications. In: Tesler, G., Durand, D. (eds.) RECMOB-CG 2007. LNCS (LNBI), vol. 4751, pp. 122–135. Springer, Heidelberg (2007)

    Chapter  Google Scholar 

  17. Page, R.D.: Maps between trees and cladistic analysis of historical associations among genes, organisms, and areas. Syst. Biol. 43, 58–77 (1994)

    Article  Google Scholar 

  18. Vernot, B., Stolzer, M., Goldman, A., Durand, D.: Reconciliation with non-binary species tree. In: CSB 2007 pp. 441–452 (2007)

    Google Scholar 

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Author information

Authors and Affiliations

  1. Department of Mathematics, Simon Fraser University, 8888 University Drive, V5A 1S6, Burnaby (BC), Canada

    Cedric Chauve

  2. DIRO, Université de Montréal, CP6128, succ. Centre-Ville, H3C 3J7, Montréal (QC), Canada

    Jean-Philippe Doyon & Sylvie Hamel

Authors
  1. Jean-Philippe Doyon
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  2. Cedric Chauve
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  3. Sylvie Hamel
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Editor information

Editors and Affiliations

  1. Molecular and Cell Biology, University of Connecticut, Division of Genetics and Genomics, Beach Hall, 354 Mansfiled Rd, CT 06269, Storrs, USA

    Craig E. Nelson

  2. Université Paris-Est, IGM-LabInfo, 5 Bd Descartes, Champs sur Marne, 77454, Marne la Vallée, France

    Stéphane Vialette

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© 2008 Springer-Verlag Berlin Heidelberg

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Doyon, JP., Chauve, C., Hamel, S. (2008). Algorithms for Exploring the Space of Gene Tree/Species Tree Reconciliations. In: Nelson, C.E., Vialette, S. (eds) Comparative Genomics. RECOMB-CG 2008. Lecture Notes in Computer Science(), vol 5267. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-87989-3_1

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  • DOI: https://doi.org/10.1007/978-3-540-87989-3_1

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-87988-6

  • Online ISBN: 978-3-540-87989-3

  • eBook Packages: Computer ScienceComputer Science (R0)

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