PHYLO-ASP: Phylogenetic Systematics with Answer Set Programming

  • Esra Erdem
Part of the Lecture Notes in Computer Science book series (LNCS, volume 5753)

Abstract

This note summarizes the use of Answer Set Programming to solve various computational problems to infer phylogenetic trees and phylogenetic networks, and discusses its applicability and effectiveness on some real taxa.

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. 1.
    Hennig, W.: Phylogenetic Systematics. University of Illinois Press (1966); by Davis, D.D., Zangerl, R.: Translated from Grundzuege einer Theorie der phylogenetischen Systematik (1950)Google Scholar
  2. 2.
    Brooks, D.R., Erdem, E., Minett, J.W., Ringe, D.: Character-based cladistics and answer set programming. In: Hermenegildo, M.V., Cabeza, D. (eds.) PADL 2004. LNCS, vol. 3350, pp. 37–51. Springer, Heidelberg (2005)Google Scholar
  3. 3.
    Erdem, E., Wang, F.: Reconstructing the evolutionary history of Chinese dialects. Accepted for presentation at the 39th International Conference on Sino-Tibetan Languages and Linguistics, ICSTLL 2006(2006)Google Scholar
  4. 4.
    Brooks, D.R., Erdem, E., Erdoğan, S.T., Minett, J.W., Ringe, D.: Inferring phylogenetic trees using answer set programming. Journal of Automated Reasoning 39(4), 471–511 (2007)MATHCrossRefMathSciNetGoogle Scholar
  5. 5.
    Erdem, E., Lifschitz, V., Nakhleh, L., Ringe, D.: Reconstructing the evolutionary history of Indo-European languages using answer set programming. In: Dahl, V., Wadler, P. (eds.) PADL 2003. LNCS, vol. 2562, pp. 160–176. Springer, Heidelberg (2003)CrossRefGoogle Scholar
  6. 6.
    Erdem, E., Lifschitz, V., Ringe, D.: Temporal phylogenetic networks and logic programming. Theory and Practice of Logic Programming 6(5), 539–558 (2006)MATHCrossRefMathSciNetGoogle Scholar
  7. 7.
    Mair, V.H. (ed.): The Bronze Age and Early Iron Age Peoples of Eastern Central Asia. Institute for the Study of Man, Washington (1998)Google Scholar
  8. 8.
    Mallory, J.P.: In Search of the Indo-Europeans. Thames and Hudson, London (1989)Google Scholar
  9. 9.
    Roberts, R.G., Jones, R.M., Smith, M.A.: Thermoluminescence dating of a 50,000-year-old human occupation site in Northern Australia. Science 345, 153–156 (1990)Google Scholar
  10. 10.
    White, J.P., O’Connell, J.F.: A Prehistory of Australia, New Guinea, and Sahul. Academic Press, New York (1982)Google Scholar
  11. 11.
    Brooks, D.R., McLennan, D.A.: Phylogeny, Ecology, and Behavior: A Research Program in Comparative Biology. Univ. Chicago Press, Chicago (1991)Google Scholar
  12. 12.
    Brooks, D.R., Mayden, R.L., McLennan, D.A.: Phylogeny and biodiversity: Conserving our evolutionary legacy. Trends in Ecology and Evolution 7, 55–59 (1992)CrossRefGoogle Scholar
  13. 13.
    Day, W.H.E., Sankoff, D.: Computational complexity of inferring phylogenies by compatibility. Systematic Zoology 35(2), 224–229 (1986)CrossRefGoogle Scholar
  14. 14.
    Minett, J.W., Wang, W.S.Y.: On detecting borrowing: distance-based and character-based approaches. Diachronica 20(2), 289–330 (2003)CrossRefGoogle Scholar
  15. 15.
    Ringe, D., Warnow, T., Taylor, A.: Indo-European and computational cladistics. Transactions of the Philological Society 100(1), 59–129 (2002)CrossRefGoogle Scholar
  16. 16.
    Hoberg, E.P.: Congruent and synchronic patterns in biogeography and speciation among seabirds, pinnipeds, ans cestodes. J. Parasitology 78(4), 601–615 (1992)CrossRefGoogle Scholar
  17. 17.
    Chandler, R.M.: Phylogenetic analysis of the alcids. PhD thesis, University of Kansas (1990)Google Scholar
  18. 18.
    Cakmak, D., Erdem, E., Erdogan, H.: Computing weighted solutions in answer set programming. In: Proc. of LPNMR (to appear, 2009)Google Scholar
  19. 19.
    Eiter, T., Erdem, E., Erdogan, H., Fink, M.: Finding similar or diverse solutions in answer set programming. In: Proc. of ICLP (to appear, 2009)Google Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2009

Authors and Affiliations

  • Esra Erdem
    • 1
  1. 1.Faculty of Engineering and Natural SciencesSabancı UniversityIstanbulTurkey

Personalised recommendations