Journal of Automated Reasoning

, 39:471

Inferring Phylogenetic Trees Using Answer Set Programming


  • Daniel R. Brooks
    • Department of Ecology and Evolutionary BiologyUniversity of Toronto
    • Faculty of Engineering and Natural SciencesSabancı University
  • Selim T. Erdoğan
    • Department of Computer SciencesUniversity of Texas at Austin
  • James W. Minett
    • Department of Electronic EngineeringChinese University of Hong Kong
  • Don Ringe
    • Department of LinguisticsUniversity of Pennsylvania

DOI: 10.1007/s10817-007-9082-1

Cite this article as:
Brooks, D.R., Erdem, E., Erdoğan, S.T. et al. J Autom Reasoning (2007) 39: 471. doi:10.1007/s10817-007-9082-1


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.


Answer set programmingPhylogenyCladistics

Copyright information

© Springer Science+Business Media B.V. 2007