Abstract
We provide a unifying view on the structure of maximum (acyclic) agreement forests of rooted and unrooted phylogenies. This enables us to obtain linear- or O(n log n)-time 3-approximation and improved fixed-parameter algorithms for the subtree prune and regraft distance between two rooted phylogenies, the tree bisection and reconnection distance between two unrooted phylogenies, and the hybridization number of two rooted phylogenies.
For details, see [18].
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References
Allen, B.L., Steel, M.: Subtree transfer operations and their induced metrics on evolutionary trees. Annals of Comb. 5, 1–15 (2001)
Baroni, M., Grünewald, S., Moulton, V., Semple, C.: Bounding the number of hybridisation events for a consistent evolutionary history. J. Math. Biol. 51, 171–182 (2005)
Beiko, R.G., Hamilton, N.: Phylogenetic identification of lateral genetic transfer events. BMC Evol. Biol. 6, 15 (2006)
Bonet, M.L., St. John, K., Mahindru, R., Amenta, N.: Approximating subtree distances between phylogenies. J. Comp. Biol. 13, 1419–1434 (2006)
Bordewich, M., McCartin, C., Semple, C.: A 3-approximation algorithm for the subtree distance between phylogenies. J. Disc. Alg. 6, 458–471 (2008)
Bordewich, M., Semple, C.: On the computational complexity of the rooted subtree prune and regraft distance. Annals of Comb. 8, 409–423 (2005)
Bordewich, M., Semple, C.: Computing the hybridization number of two phylogenetic trees is fixed-parameter tractable. IEEE/ACM Trans. on Comp. Biol. and Bioinf. 4, 458–466 (2007)
Bordewich, M., Semple, C.: Computing the minimum number of hybridization events for a consistent evolutionary history. Disc. Appl. Math. 155, 914–928 (2007)
Chataigner, F.: Approximating the maximum agreement forest on k trees. Inf. Proc. Letters 93, 239–244 (2005)
Hallett, M., McCartin, C.: A faster FPT algorithm for the maximum agreement forest problem. Theory of Comp. Sys. 41, 539–550 (2007)
Hein, J., Jiang, T., Wang, L., Zhang, K.: On the complexity of comparing evolutionary trees. Disc. Appl. Math. 71, 153–169 (1996)
Hickey, G., Dehne, F., Rau-Chaplin, A., Blouin, C.: SPR distance computation for unrooted trees. Evol. Bioinf. 4, 17–27 (2008)
Hillis, D.M., Heath, T.A., St. John, K.: Analysis and visualization of tree space. Syst. Biol. 54, 471–482 (2005)
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, 523–536 (1997)
Nakhleh, L., Warnow, T., Lindner, C.R., St. John, K.: Reconstructing reticulate evolution in species—theory and practice. J. Comp. Biol. 12, 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, 91–110 (2007)
Whidden, C., Zeh, N.: A unifying view on approximation and FPT of agreement forests (2009), http://www.cs.dal.ca/~nzeh/Publications/maf.pdf
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Whidden, C., Zeh, N. (2009). A Unifying View on Approximation and FPT of Agreement Forests. In: Salzberg, S.L., Warnow, T. (eds) Algorithms in Bioinformatics. WABI 2009. Lecture Notes in Computer Science(), vol 5724. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-04241-6_32
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DOI: https://doi.org/10.1007/978-3-642-04241-6_32
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