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Issue No.03 - July-September (2010 vol.7)
pp: 572-576
Maria Luisa Bonet , Universitat Politècnica de Catalunya (UPC), Barcelona
Katherine St. John , City University of New York (CUNY), Bronx
We show that subtree prune and regraft (uSPR) distance on unrooted trees is fixed parameter tractable with respect to the distance. We also make progress on a conjecture of Steel [9] on the preservation of uSPR distance under chain reduction, improving on lower bounds of Hickey et al. [7].
Phylogeny, analysis of algorithms, fixed parameter tractability.
Maria Luisa Bonet, Katherine St. John, "On the Complexity of uSPR Distance", IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol.7, no. 3, pp. 572-576, July-September 2010, doi:10.1109/TCBB.2008.132
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[7] G. Hickey, F. Dehne, A. Rau-Chaplin, and C. Blouin, "SPR Distance Computation for Unrooted Trees," Evolutionary Bioinformatics, vol. 4, pp. 17-27, 2008.
[8] C. McCartin, personal comm., 2008.
[9] M. Steel, "SPR Conjecture," research reward2.pdf, 2002.
[10] D.L. Swofford, G.J. Olsen, P.J. Waddell, and D.M. Hillis, "Phylogenetic Inference," Molecular Systematics, second ed., pp. 407-514, Sinauer, 1996.
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