Algorithmica

, Volume 74, Issue 3, pp 1019–1054 | Cite as

Fixed-Parameter and Approximation Algorithms for Maximum Agreement Forests of Multifurcating Trees

Article

Abstract

We present efficient fixed-parameter and approximation algorithms for the NP-hard problem of computing a maximum agreement forest (MAF) of a pair of multifurcating (nonbinary) rooted trees. Multifurcating trees arise naturally as a result of statistical uncertainty in current tree construction methods. The size of an MAF corresponds to the subtree prune-and-regraft distance of the two trees and is intimately connected to their hybridization number. These distance measures are essential tools for understanding reticulate evolution, such as lateral gene transfer, recombination, and hybridization. Our algorithms nearly match the running times of the currently best algorithms for the binary case. This is achieved using a combination of efficient branching rules (similar to but more complex than in the binary case) and a novel edge protection scheme that further reduces the size of the search space the algorithms need to explore.

Keywords

Phylogenetics Fixed-parameter tractability Approximation algorithms 

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Copyright information

© Springer Science+Business Media New York 2015

Authors and Affiliations

  1. 1.Program in Computational BiologyFred Hutchinson Cancer Research CenterSeattleUSA
  2. 2.Faculty of Computer ScienceDalhousie UniversityHalifaxCanada

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