Inferring phylogenetic trees using answer set programming

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Brooks, Dan and Erdem, Esra and Erdoğan, Selim and Minett, James and Ringe, Don (2007) Inferring phylogenetic trees using answer set programming. Journal of Automated Reasoning, 39 (4). pp. 471-511. ISSN 0168-7433 (Print) 1573-0670 (Online)

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Abstract

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 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.
Item Type: Article
Divisions: Faculty of Engineering and Natural Sciences
Depositing User: Esra Erdem
Date Deposited: 26 Nov 2007 09:12
Last Modified: 25 May 2011 14:04
URI: https://research.sabanciuniv.edu/id/eprint/7208

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