Inferring Phylogenetic Trees Using Answer Set Programming

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: to historical analysis of languages, and to 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 ∗ This paper is a revised and extended version of [3]. 1 

• Type: Journal
• Year: 2007
• Where: JAR
• Authors: Daniel R. Brooks, Esra Erdem, Selim T. Erdogan, James W. Minett, Donald Ringe
• Keywords: Computational Method, Historical Analysis, JAR 2007, Plausible Phylogenies