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Solving the Tree Containment Problem for Genetically Stable Networks in Quadratic Time

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Combinatorial Algorithms (IWOCA 2015)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 9538))

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Abstract

A phylogenetic network is a rooted acyclic digraph whose leaves are labeled with a set of taxa. The tree containment problem is a fundamental problem arising from model validation in the study of phylogenetic networks. It asks to determine whether or not a given network displays a given phylogenetic tree over the same leaf set. It is known to be NP-complete in general. Whether or not it remains NP-complete for stable networks is an open problem. We make progress towards answering that question by presenting a quadratic time algorithm to solve the tree containment problem for a new class of networks that we call genetically stable networks, which include tree-child networks and comprise a subclass of stable networks.

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Notes

  1. 1.

    See e.g. the network given at http://phylnet.info/isiphync/network.php?id=4.

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Acknowledgments

The project was financially supported by Merlion Programme 2013.

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Authors and Affiliations

  1. Université Paris-Est, LIGM (UMR 8049), UPEM, CNRS, ESIEE, ENPC, 77454, Marne-la-Vallée, France

    Philippe Gambette, Anthony Labarre & Stéphane Vialette

  2. Department of Mathematics, National University of Singapore, Singapore, 119076, Singapore

    Andreas D. M. Gunawan & Louxin Zhang

Authors
  1. Philippe Gambette
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  2. Andreas D. M. Gunawan
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  3. Anthony Labarre
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  4. Stéphane Vialette
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  5. Louxin Zhang
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Corresponding author

Correspondence to Philippe Gambette .

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Editors and Affiliations

  1. Dept. of Computer Science, University of Verona, Verona, Italy

    Zsuzsanna Lipták

  2. Dept. of Computing and Software, McMaster University, Hamilton, Canada

    William F. Smyth

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Gambette, P., Gunawan, A.D.M., Labarre, A., Vialette, S., Zhang, L. (2016). Solving the Tree Containment Problem for Genetically Stable Networks in Quadratic Time. In: Lipták, Z., Smyth, W. (eds) Combinatorial Algorithms. IWOCA 2015. Lecture Notes in Computer Science(), vol 9538. Springer, Cham. https://doi.org/10.1007/978-3-319-29516-9_17

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  • DOI: https://doi.org/10.1007/978-3-319-29516-9_17

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  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-29515-2

  • Online ISBN: 978-3-319-29516-9

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