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A Duality Based 2-Approximation Algorithm for Maximum Agreement Forest

Authors Frans Schalekamp, Anke van Zuylen, Suzanne van der Ster

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Frans Schalekamp
Anke van Zuylen
Suzanne van der Ster

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Frans Schalekamp, Anke van Zuylen, and Suzanne van der Ster. A Duality Based 2-Approximation Algorithm for Maximum Agreement Forest. In 43rd International Colloquium on Automata, Languages, and Programming (ICALP 2016). Leibniz International Proceedings in Informatics (LIPIcs), Volume 55, pp. 70:1-70:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2016)
https://doi.org/10.4230/LIPIcs.ICALP.2016.70

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.
Keywords
  • Maximum agreement forest
  • phylogenetic tree
  • SPR distance
  • subtree prune-and-regraft distance
  • computational biology

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