Of chicken teeth and mouse eyes, or generalized character compatibility

  • Craig Benham
  • Sampath Kannan
  • Tandy Warnow
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 937)


We propose a new model of computation for deriving phylogenetic trees based upon a generalization of qualitative characters. The model we propose is based upon recent experimental research in molecular biology. We show that the general case of determining perfect compatibility of generalized ordered characters is an NP-Complete problem, but can be solved in polynomial time for a special case.


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  1. 1.
    R. Agarwala, and D. Fernández-Baca, (1994), Fast and simple algorithms for perfect phytogeny and triangulating colored graphs, DIMACS Tech Report # 94-51.Google Scholar
  2. 2.
    Agarwala, R. and D. Fernandez-Baca (1994), A Polynomial-time Algorithm for the Perfect Phylogeny Problem when the Number of Character States is Fixed. SIAM J. on Computing, Vol. 23 No. 6, pp. 1216–1224.CrossRefGoogle Scholar
  3. 3.
    Alberts, B., Bray, D., Lewis, J., Raff, M., Roberts, K. and Watson, J.D. (1989) The Molecular Biology of the Cell, 2nd Ed., Garland Publishing Inc., New York, pp. 485–488.Google Scholar
  4. 4.
    H. Bodlaender, M. Fellows, and T. Warnow (1992), Two strikes against perfect phylogeny, Proceedings of the 19th International Colloquium on Automata, Languages, and Programming, Springer Verlag, Lecture Notes in Computer Science, pp. 273–283.Google Scholar
  5. 5.
    J. Felsenstein (1982), Numerical methods for inferring evolutionary trees, The Quarterly Review of Biology, Vol. 57, No. 4.Google Scholar
  6. 6.
    Janis, C. (1994) The Sabertooth's Repeat Performances Nat'l. Hist., 103 pp. 78–82.Google Scholar
  7. 7.
    S. Kannan and T. Warnow (1994), Inferring evolutionary history from DNA sequences, SIAM J. on Computing, Vol. 23, Nov. 4, pp. 713–737.CrossRefGoogle Scholar
  8. 8.
    S. Kannan and T. Warnow, A fast algorithm for the computation and enumeration of perfect phylogenies, Proceedings, ACM-SIAM Symposium on Discrete Algorithms, San Francisco, 1995, pp. 595–603.Google Scholar
  9. 9.
    Kollar, E.J. and Fisher, C. (1980) Tooth Induction in Chick Epithelium: Expression of Quiescent Genes for Enamel Synthesis Science 207, pp. 993–995.PubMedGoogle Scholar
  10. 10.
    F.R. McMorris, T. Warnow, and T. Wimer (1994), Triangulating vertex colored graphs, SIAM J. Discrete Mathematics, Vol. 7 No. 2, pp. 296–306.CrossRefGoogle Scholar
  11. 11.
    Michael Steel (1992), The Complexity of Reconstructing Trees from Qualitative Characters and Subtrees, Journal of Classification, Vol. 9, pp. 91–116.Google Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 1995

Authors and Affiliations

  • Craig Benham
    • 1
  • Sampath Kannan
    • 2
  • Tandy Warnow
    • 2
  1. 1.Department of BiomathematicsMt. Sinai School of MedicineUSA
  2. 2.Department of Computer and Information SciencesUniversity of PennsylvaniaUSA

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