Encyclopedia of Algorithms

Editors: Ming-Yang Kao

Perfect Phylogeny (Bounded Number of States)

1997; Kannan, Warnow
  • Jesper Jansson
Reference work entry
DOI: https://doi.org/10.1007/978-0-387-30162-4_288

Keywords and Synonyms

Compatibility of characters with a bounded number of states; Convex tree-realization of partitions containing a bounded number of sets            

Problem Definition

Let \( { S = \{s_1,s_2,\dots,s_n\} } \)

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Notes

Acknowledgments

Supported in part by Kyushu University, JSPS (Japan Society for the Promotion of Science), and INRIA Lille – Nord Europe.

Recommended Reading

  1. 1.
    Agarwala, R., Fernández-Baca, D.: A polynomial-time algorithm for the perfect phylogeny problem when the number of character states is fixed. SIAM J. Comput. 23, 1216–1224 (1994)MathSciNetGoogle Scholar
  2. 2.
    Bodlaender, H.L., Fellows, M.R., Warnow, T.: Two strikes against perfect phylogeny. In: Proceedings of the 19th International Colloquium on Automata, Languages and Programming (ICALP 1992). Lecture Notes in Computer Science, vol. 623, pp. 273–283. Springer, Berlin (1992)Google Scholar
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    Dress, A., Steel, M.: Convex tree realizations of partitions. Appl. Math. Lett. 5, 3–6 (1992)MathSciNetGoogle Scholar
  4. 4.
    Felsenstein, J.: Inferring Phylogenies. Sinauer Associates, Inc. Sunderland, Massachusetts (2004)Google Scholar
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    Fernández-Baca, D.: The Perfect Phylogeny Problem. In: Cheng, X., Du D.-Z. (eds.) Steiner Trees in Industry, pp. 203–234. Kluwer Academic Publishers, Dordrecht, Netherlands (2001)Google Scholar
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    Fernández-Baca, D., Lagergren, J.: A polynomial-time algorithm for near-perfect phylogeny. SIAM J. Comput. 32, 1115–1127 (2003)MathSciNetGoogle Scholar
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    Gusfield, D.M.: Efficient algorithms for inferring evolutionary trees. Networks 21, 19–28 (1991)MathSciNetGoogle Scholar
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    Kanj, I.A., Nakhleh, L., Xia, G.: Reconstructing evolution of natural languages: Complexity and parametrized algorithms. In: Proceedings of the 12th Annual International Computing and Combinatorics Conference (COCOON 2006). Lecture Notes in Computer Science, vol. 4112, pp. 299–308. Springer, Berlin (2006)Google Scholar
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    Kannan, S., Warnow, T.: Inferring evolutionary history from DNA sequences. SIAM J. Comput. 23, 713–737 (1994)MathSciNetGoogle Scholar
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    Kannan, S., Warnow, T.: A fast algorithm for the computation and enumeration of perfect phylogenies. SIAM J. Comput. 26, 1749–1763 (1997)MathSciNetGoogle Scholar
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    McMorris, F.R.: On the compatibility of binary qualitative taxonomic characters. Bull. Math. Biol. 39, 133–138 (1977)MathSciNetGoogle Scholar
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    Setubal, J.C., Meidanis, J.: Introduction to Computational Molecular Biology. PWS Publishing Company, Boston (1997)Google Scholar
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    Steel, M.A.: The complexity of reconstructing trees from qualitative characters and subtrees. J. Classification 9, 91–116 (1992)MathSciNetGoogle Scholar
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    Warnow, T., Ringe, D., Taylor, A.: Reconstructing the evolutionary history of natural languages. In: Proceedings of the 7th Annual ACM-SIAM Symposium on Discrete Algorithms (SODA'96), pp. 314–322 (1996)Google Scholar

Copyright information

© Springer-Verlag 2008

Authors and Affiliations

  • Jesper Jansson
    • 1
  1. 1.Ochanomizu UniversityTokyoJapan