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Efficiently Calculating Evolutionary Tree Measures Using SAT

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Theory and Applications of Satisfiability Testing - SAT 2009 (SAT 2009)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 5584))

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Abstract

We develop techniques to calculate important measures in evolutionary biology by encoding to CNF formulas and using powerful SAT solvers. Comparing evolutionary trees is a necessary step in tree reconstruction algorithms, locating recombination and lateral gene transfer, and in analyzing and visualizing sets of trees. We focus on two popular comparison measures for trees: the hybridization number and the rooted subtree-prune-and-regraft (rSPR) distance. Both have recently been shown to be NP-hard, and efficient algorithms are needed to compute and approximate these measures. We encode these as a Boolean formula such that two trees have hybridization number k (or rSPR distance k) if and only if the corresponding formula is satisfiable. We use state-of-the-art SAT solvers to determine if the formula encoding the measure has a satisfying assignment. Our encoding also provides a rich source of real-world SAT instances, and we include a comparison of several recent solvers (minisat, adaptg2wsat, novelty+p, Walksat, March KS and SATzilla).

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Author information

Authors and Affiliations

  1. Lenguajes y Sistemas Informáticos, Universidad Politécnica de Cataluña, Spain

    María Luisa Bonet

  2. Math & Computer Science Dept., Lehman College, City U., New York, USA

    Katherine St. John

Authors
  1. María Luisa Bonet
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  2. Katherine St. John
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Editor information

Editors and Affiliations

  1. Computer Science Department, Swansea University, Faraday Building, Singleton Park, SA2 8PP, Swansea, UK

    Oliver Kullmann

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Bonet, M.L., John, K.S. (2009). Efficiently Calculating Evolutionary Tree Measures Using SAT. In: Kullmann, O. (eds) Theory and Applications of Satisfiability Testing - SAT 2009. SAT 2009. Lecture Notes in Computer Science, vol 5584. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-02777-2_3

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  • DOI: https://doi.org/10.1007/978-3-642-02777-2_3

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-02776-5

  • Online ISBN: 978-3-642-02777-2

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