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Inferring Phylogenetic Trees Using Answer Set Programming

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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: 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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Author information

Authors and Affiliations

  1. Department of Ecology and Evolutionary Biology, University of Toronto, Ontario, Canada

    Daniel R. Brooks

  2. Faculty of Engineering and Natural Sciences, Sabancı University, Istanbul, Turkey

    Esra Erdem

  3. Department of Computer Sciences, University of Texas at Austin, Austin, TX, USA

    Selim T. Erdoğan

  4. Department of Electronic Engineering, Chinese University of Hong Kong, Shatin, Hong Kong

    James W. Minett

  5. Department of Linguistics, University of Pennsylvania, Philadelphia, PA, USA

    Don Ringe

Authors
  1. Daniel R. Brooks
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  2. Esra Erdem
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  3. Selim T. Erdoğan
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  4. James W. Minett
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  5. Don Ringe
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Corresponding author

Correspondence to Esra Erdem.

Additional information

This paper is a revised and extended version of [3].

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Brooks, D.R., Erdem, E., Erdoğan, S.T. et al. Inferring Phylogenetic Trees Using Answer Set Programming. J Autom Reasoning 39, 471–511 (2007). https://doi.org/10.1007/s10817-007-9082-1

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  • DOI: https://doi.org/10.1007/s10817-007-9082-1

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