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DOI: 10.4230/LIPIcs.ICALP.2016.70
URN: urn:nbn:de:0030-drops-62149
URL: http://drops.dagstuhl.de/opus/volltexte/2016/6214/
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Schalekamp, Frans ; van Zuylen, Anke ; van der Ster, Suzanne

A Duality Based 2-Approximation Algorithm for Maximum Agreement Forest

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LIPIcs-ICALP-2016-70.pdf (0.6 MB)


Abstract

We give a 2-approximation algorithm for the Maximum Agreement Forest problem on two rooted binary trees. This NP-hard problem has been studied extensively in the past two decades, since it can be used to compute the Subtree Prune-and-Regraft (SPR) distance between two phylogenetic trees. Our result improves on the very recent 2.5-approximation algorithm due to Shi, Feng, You and Wang (2015). Our algorithm is the first approximation algorithm for this problem that uses LP duality in its analysis.

BibTeX - Entry

@InProceedings{schalekamp_et_al:LIPIcs:2016:6214,
  author =	{Frans Schalekamp and Anke van Zuylen and Suzanne van der Ster},
  title =	{{A Duality Based 2-Approximation Algorithm for Maximum Agreement Forest}},
  booktitle =	{43rd International Colloquium on Automata, Languages, and Programming (ICALP 2016)},
  pages =	{70:1--70:14},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-013-2},
  ISSN =	{1868-8969},
  year =	{2016},
  volume =	{55},
  editor =	{Ioannis Chatzigiannakis and Michael Mitzenmacher and Yuval Rabani and Davide Sangiorgi},
  publisher =	{Schloss Dagstuhl--Leibniz-Zentrum fuer Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{http://drops.dagstuhl.de/opus/volltexte/2016/6214},
  URN =		{urn:nbn:de:0030-drops-62149},
  doi =		{10.4230/LIPIcs.ICALP.2016.70},
  annote =	{Keywords: Maximum agreement forest, phylogenetic tree, SPR distance, subtree prune-and-regraft distance, computational biology}
}

Keywords: Maximum agreement forest, phylogenetic tree, SPR distance, subtree prune-and-regraft distance, computational biology
Seminar: 43rd International Colloquium on Automata, Languages, and Programming (ICALP 2016)
Issue Date: 2016
Date of publication: 17.08.2016


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