Inferring Phylogenetic Trees Using Answer Set Programming

  • Daniel R. Brooks
  • Esra Erdem
  • Selim T. Erdoğan
  • James W. Minett
  • Don Ringe
Article

Abstract

We describe the reconstruction of a phylogeny for a set of taxa, with a character-based cladistics approach, in a declarative knowledge representation formalism, and show how to use computational methods of answer set programming to generate conjectures about the evolution of the given taxa. We have applied this computational method in two domains: historical analysis of languages and historical analysis of parasite-host systems. In particular, using this method, we have computed some plausible phylogenies for Chinese dialects, for Indo-European language groups, and for Alcataenia species. Some of these plausible phylogenies are different from the ones computed by other software. Using this method, we can easily describe domain-specific information (e.g., temporal and geographical constraints), and thus prevent the reconstruction of some phylogenies that are not plausible.

Keywords

Answer set programming Phylogeny Cladistics 

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Copyright information

© Springer Science+Business Media B.V. 2007

Authors and Affiliations

  • Daniel R. Brooks
    • 1
  • Esra Erdem
    • 2
  • Selim T. Erdoğan
    • 3
  • James W. Minett
    • 4
  • Don Ringe
    • 5
  1. 1.Department of Ecology and Evolutionary BiologyUniversity of TorontoOntarioCanada
  2. 2.Faculty of Engineering and Natural SciencesSabancı UniversityIstanbulTurkey
  3. 3.Department of Computer SciencesUniversity of Texas at AustinAustinUSA
  4. 4.Department of Electronic EngineeringChinese University of Hong KongShatinHong Kong
  5. 5.Department of LinguisticsUniversity of PennsylvaniaPhiladelphiaUSA

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