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Local Search for the Maximum Parsimony Problem

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Advances in Natural Computation (ICNC 2005)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 3612))

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Abstract

Four local search algorithms are investigated for the phylogenetic tree reconstruction problem under the Maximum Parsimony criterion. A new subtree swapping neighborhood is introduced and studied in combination with an effective array-based tree representation. Computational results are shown on a set of randomly generated benchmark instances as well as on 8 real problems (sequences of phytopathogen γ-proteobacteria) and compared with two references from the literature.

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References

  1. Andreatta, A.A., Ribeiro, C.C.: Heuristics for the phylogeny problem. Journal of Heuristics 8, 429–447 (2002)

    Article  MATH  Google Scholar 

  2. Barker, D.: LVB: parsimony and simulated annealing in the search for phylogenetic trees. Bioinformatics 20, 274–275 (2003)

    Article  Google Scholar 

  3. Camin, J.H., Sokal, R.R.: A method for deucing branching sequences in phylogeny. Evolution 19, 311–326 (1965)

    Article  Google Scholar 

  4. Felsenstein, J.: Phylogenetic Inference Package (PHYLIP) (1993)

    Google Scholar 

  5. Felsenstein, J.: Inferring Phylogenies. Sinauer (2003)

    Google Scholar 

  6. Fitch, W.: Towards defining course of evolution: minimum change for a specified tree topology. Systematic Zoology 20, 406–416 (1971)

    Article  Google Scholar 

  7. Foulds, L.R., Graham, R.L.: The Steiner problem in phylogeny is NP-complete. Advances in Applied Mathematics 3, 43–49 (1982)

    Article  MATH  MathSciNet  Google Scholar 

  8. Gascuel, O.: BIONJ: An improved version of the NJ algorithm based on a simple model of sequence data. Molecular Biology and Evolution 14, 685–695 (1997)

    Google Scholar 

  9. Kimura, M.: A simple model for estimating evolutionary rates of base of base substitutions through comparative studies of nucleotide sequence. Journal of Molecular Evolution 16, 111–120 (1980)

    Article  Google Scholar 

  10. Kuhner, M.K., Felsenstein, J.: A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates. Molecular Biology and Evolution 11, 459–468 (1994); Erratum 12, 525 (1995)

    Google Scholar 

  11. Saitou, N., Nei, M.: Neighbor-joining method: A new method for reconstructing phylogenetic trees. Molecular Biology and Evolution 4, 406–425 (1987)

    Google Scholar 

  12. Swofford, D.L.: PAUP: Phylogenetic analysis using parsimony. Sinauer Associates (1998)

    Google Scholar 

  13. Swofford, D.L., Olsen, G.J.: Phylogeny Reconstruction. In: Hillis, D.M., Moritz, C. (eds.) Molecular Systematics, ch. 11, pp. 411–501 (1990)

    Google Scholar 

  14. Waterman, M.S., Smith, T.F.: On the similarity of dendograms. Journal of Theoretical Biology 73, 789–800 (1978)

    Article  MathSciNet  Google Scholar 

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Author information

Authors and Affiliations

  1. LERIA, University of Angers, 2 Boulevard Lavoisier, 49045, Angers Cedex 01, France

    Adrien Goëffon, Jean-Michel Richer & Jin-Kao Hao

Authors
  1. Adrien Goëffon
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  2. Jean-Michel Richer
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  3. Jin-Kao Hao
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Editor information

Editors and Affiliations

  1. School of Electrical and Electronic Engineering, Nanyang Technological University, Block S1, Nanyang Avenue, 639798, Singapore

    Lipo Wang

  2. School of Software, Sun Yat-Sen University, 510275, Guangzhou, China

    Ke Chen

  3. School of Computer Engineering, Nanyang Technological University, BLK N4, 2b-39, Nanyang Avenue, 639798, Singapore

    Yew Soon Ong

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© 2005 Springer-Verlag Berlin Heidelberg

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Goëffon, A., Richer, JM., Hao, JK. (2005). Local Search for the Maximum Parsimony Problem. In: Wang, L., Chen, K., Ong, Y.S. (eds) Advances in Natural Computation. ICNC 2005. Lecture Notes in Computer Science, vol 3612. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11539902_83

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  • DOI: https://doi.org/10.1007/11539902_83

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-28320-1

  • Online ISBN: 978-3-540-31863-7

  • eBook Packages: Computer ScienceComputer Science (R0)

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