Journal of Automated Reasoning

, Volume 39, Issue 4, pp 471-511

First online:

Inferring Phylogenetic Trees Using Answer Set Programming

  • Daniel R. BrooksAffiliated withDepartment of Ecology and Evolutionary Biology, University of Toronto
  • , Esra ErdemAffiliated withFaculty of Engineering and Natural Sciences, Sabancı University Email author 
  • , Selim T. ErdoğanAffiliated withDepartment of Computer Sciences, University of Texas at Austin
  • , James W. MinettAffiliated withDepartment of Electronic Engineering, Chinese University of Hong Kong
  • , Don RingeAffiliated withDepartment of Linguistics, University of Pennsylvania

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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 programming Phylogeny Cladistics