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International Conference on Algorithms for Computational Biology

AlCoB 2015: Algorithms for Computational Biology pp 141–153Cite as

Constructing Parsimonious Hybridization Networks from Multiple Phylogenetic Trees Using a SAT-Solver

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Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 9199))

Abstract

We present an exact algorithm for constructing minimal hybridization networks from multiple trees which is based on reducing the problem to the Boolean satisfiability problem. The main idea of our algorithm is to iterate over possible hybridization numbers and to construct a Boolean formula for each of them that is satisfiable iff there exists a network with such hybridization number. The proposed algorithm is implemented in a software tool PhyloSAT. The experimental evaluation of our algorithm on biological data shows that our method is as far as we know the fastest exact algorithm for the minimal hybridization network construction problem.

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Notes

  1. 1.

    https://github.com/ctlab/PhyloSAT.

  2. 2.

    http://www.msoos.org/cryptominisat4/.

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Acknowledgements

This work was financially supported by the Government of Russian Federation, Grant 074-U01. Authors would like to thank Igor Buzhinsky, Daniil Chivilikhin and Fedor Tsarev for helpful comments and conversations.

Author information

Authors and Affiliations

  1. ITMO University, Saint Petersburg, Russia

    Vladimir Ulyantsev & Mikhail Melnik

Authors
  1. Vladimir Ulyantsev
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  2. Mikhail Melnik
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Corresponding author

Correspondence to Vladimir Ulyantsev .

Editor information

Editors and Affiliations

  1. Research Group on Mathematical Linguistics, Rovira i Virgili University, Tarragona, Spain

    Adrian-Horia Dediu

  2. Faculty of Science, National Autonomous University of Mexico - UNAM, Mexico City, Mexico

    Francisco Hernández-Quiroz

  3. Research Group on Mathematical Linguistics, Rovira i Virgili University, Tarragona, Spain

    Carlos Martín-Vide

  4. Institute for Research in Applied Mathematics and Systems – IIMAS, National Autonomous University of Mexico - UNAM, Mexico City, Mexico

    David A. Rosenblueth

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© 2015 Springer International Publishing Switzerland

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Ulyantsev, V., Melnik, M. (2015). Constructing Parsimonious Hybridization Networks from Multiple Phylogenetic Trees Using a SAT-Solver. In: Dediu, AH., Hernández-Quiroz, F., Martín-Vide, C., Rosenblueth, D. (eds) Algorithms for Computational Biology. AlCoB 2015. Lecture Notes in Computer Science(), vol 9199. Springer, Cham. https://doi.org/10.1007/978-3-319-21233-3_11

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  • DOI: https://doi.org/10.1007/978-3-319-21233-3_11

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  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-21232-6

  • Online ISBN: 978-3-319-21233-3

  • eBook Packages: Computer ScienceComputer Science (R0)

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