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.

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Cataloged from PDF version of article.The work described in this report is motivated by the desire to test the expressive possibilities of\ud action language C+. The Causal Calculator (CCALC) is a system that answers queries about action\ud domains described in a fragment of that language. The Zoo World and the Traffic World have been\ud proposed by Erik Sandewall in his Logic Modelling Workshop—an environment for communicating\ud axiomatizations of action domains of nontrivial size.\ud The Zoo World consists of several cages and the exterior, gates between them, and animals of\ud several species, including humans. Actions in this domain include moving within and between cages,\ud opening and closing gates, and mounting and riding animals. The Traffic World includes vehicles\ud moving continuously between road crossings subject to a number of restrictions, such as speed\ud limits and keeping a fixed safety distance away from other vehicles on the road. We show how to\ud represent the two domains in the input language of CCALC, and how to use CCALC to test these\ud representations.(C)2003 Elsevier B.V. All rights reserved