Abstract
We improve on earlier FPT algorithms for computing a rooted maximum agreement forest (MAF) or a maximum acyclic agreement forest (MAAF) of a pair of phylogenetic trees. Their sizes give the subtree-prune-and-regraft (SPR) distance and the hybridization number of the trees, respectively. We introduce new branching rules that reduce the running time of the algorithms from O(3k n) and O(3k n logn) to O(2.42k n) and O(2.42k n logn), respectively. In practice, the speed up may be much more than predicted by the worst-case analysis. We confirm this intuition experimentally by computing MAFs for simulated trees and trees inferred from protein sequence data. We show that our algorithm is orders of magnitude faster and can handle much larger trees and SPR distances than the best previous methods, treeSAT and sprdist.
Details can be found in [17]
This is a preview of subscription content, log in via an institution.
Buying options
Tax calculation will be finalised at checkout
Purchases are for personal use only
Learn about institutional subscriptionsPreview
Unable to display preview. Download preview PDF.
References
Baroni, M., Grünewald, S., Moulton, V., Semple, C.: Bounding the number of hybridisation events for a consistent evolutionary history. J. Math. Biol. 51(2), 171–182 (2005)
Beiko, R.G., Harlow, T.J., Ragan, M.A.: Highways of gene sharing in prokaryotes. P. Natl. Acad. Sci. USA 102(40), 14332–14337 (2005)
Beiko, R.G., Hamilton, N.: Phylogenetic identification of lateral genetic transfer events. BMC Evol. Biol. 6(1), 15 (2006)
Bonet, M.L., John, K.S.: Efficiently Calculating Evolutionary Tree Measures Using SAT. In: Kullmann, O. (ed.) SAT 2009. LNCS, vol. 5584, pp. 4–17. Springer, Heidelberg (2009)
Bonet, M.L., John, K.S., Mahindru, R., Amenta, N.: Approximating subtree distances between phylogenies. J. Comp. Biol. 13(8), 1419–1434 (2006)
Bordewich, M., Linz, S., John, K.S., Semple, C.: A reduction algorithm for computing the hybridization number of two trees. Evol. Bioinform. 3, 86–98 (2007)
Bordewich, M., McCartin, C., Semple, C.: A 3-approximation algorithm for the subtree distance between phylogenies. J. Disc. Alg. 6(3), 458–471 (2008)
Bordewich, M., Semple, C.: On the computational complexity of the rooted subtree prune and regraft distance. Annals of Comb. 8(4), 409–423 (2005)
Bordewich, M., Semple, C.: Computing the hybridization number of two phylogenetic trees is fixed-parameter tractable. IEEE/ACM T. Comp. Biol. 4(3), 458–466 (2007)
Bordewich, M., Semple, C.: Computing the minimum number of hybridization events for a consistent evolutionary history. Disc. Appl. Math. 155(8), 914–928 (2007)
Hein, J., Jiang, T., Wang, L., Zhang, K.: On the complexity of comparing evolutionary trees. Disc. Appl. Math. 71(1-3), 153–169 (1996)
Hickey, G., Dehne, F., Rau-Chaplin, A., Blouin, C.: SPR distance computation for unrooted trees. Evol. Bioinform. 4, 17–27 (2008)
Hillis, D.M., Moritz, C., Mable, B.K. (eds.): Molecular Systematics. Sinauer Associates (1996)
Maddison, W.P.: Gene trees in species trees. Syst. Biol. 46(3), 523–536 (1997)
Nakhleh, L., Warnow, T., Lindner, C.R., John, K.S.: Reconstructing reticulate evolution in species—theory and practice. J. Comp. Biol. 12(6), 796–811 (2005)
Rodrigues, E.M., Sagot, M.F., Wakabayashi, Y.: The maximum agreement forest problem: Approximation algorithms and computational experiments. Theor. Comp. Sci. 374(1-3), 91–110 (2007)
Whidden, C., Beiko, R.G., Zeh, N.: Fast FPT algorithms for computing rooted agreement forests: Theory and experiments. Tech. Rep. CS-2010-03, Faculty of Computer Science, Dalhousie University (2010)
Whidden, C., Zeh, N.: A unifying view on approximation and FPT of agreement forests. In: Salzberg, S.L., Warnow, T. (eds.) WABI 2009. LNCS(LNBI), vol. 5724, pp. 390–401. Springer, Heidelberg (2009)
Whidden, C.: rSPR FPT Software, http://kiwi.cs.dal.ca/Software/RSPR
Wu, Y.: A practical method for exact computation of subtree prune and regraft distance. Bioinformatics 25(2), 190–196 (2009)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2010 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Whidden, C., Beiko, R.G., Zeh, N. (2010). Fast FPT Algorithms for Computing Rooted Agreement Forests: Theory and Experiments. In: Festa, P. (eds) Experimental Algorithms. SEA 2010. Lecture Notes in Computer Science, vol 6049. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-13193-6_13
Download citation
DOI: https://doi.org/10.1007/978-3-642-13193-6_13
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-13192-9
Online ISBN: 978-3-642-13193-6
eBook Packages: Computer ScienceComputer Science (R0)