Inferring Phylogenetic Trees Using Answer Set Programming (2007)
Daniel R. Brooks, Esra Erdem, Selim T. Erdogan, James W. Minett, and Donald Ringe
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.
Journal of Automated Reasoning, Vol. 39 (2007), pp. 471-511.

Esra Erdem Ph.D. Alumni esraerdem [at] sabanciuniv edu
Selim T. Erdoğan Ph.D. Alumni selim [at] cs utexas edu