Gene Trees and Species Trees: The Gene-Duplication Problem is Fixed-Parameter Tractable
Gene Duplication is the problem of computing an optimal species tree for a given set of gene trees under the Gene-Duplication Model (first introduced by Goodman et al.). The problem is known to be NP-complete. We give a fixed-parameter-tractable algorithm solving the problem parameterized by the number of gene duplications necessary to rectify the gene trees with respect to the species tree.
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- 2.R. G. Downey and M. R. Fellows. Parameterized Complexity, Springer, 1998.Google Scholar
- 3.R. Downey, M. Fellows, and U. Stege. “Parameterized Complexity: A Framework for Systematically Confronting Computational Intractability,” in The Future of Discr. Mathem.: Proc. of the 1st DIMATIA Symp., AMS-DIMACS, to appear.Google Scholar
- 4.R. G. Downey, M. R. Fellows, and U. Stege. Computational Tractability: The View From Mars, to appear in the Bulletin of the EATCS.Google Scholar
- 6.M. Fellows, M. Hallett, and U. Stege. “On the Multiple Gene Duplication Problem”, Algorithms and Computation, 9th International Symposium, ISAAC’98, LNCS 1533 (December 1998).Google Scholar
- 7.W. Fitch, E. Margoliash. “Construction of Phylogenetic Tree,” Sci. 155 (1967).Google Scholar
- 8.M. Goodman, J. Czelusniak, G. Moore, A. Romero-Herrera, G. Matsuda. “Fitting the Gene Lineage into its Species Lineage: A parsimony strategy illustrated by cladograms constructed from globin sequences,” Syst. Zool. (1979), 28.Google Scholar
- 10.J. Hein, T. Jiang, L. Wang, and K. Zhang. “On the Complexity of Comparing Evolutionary Trees”, DAMATH: Discrete Applied Mathematics and Combinatorial Operations Research and Computer Science 71 (1996).Google Scholar
- 11.B. Ma, M. Li, and L. Zhang. “On Reconstructing Species Trees from Gene Trees in Term of Duplications and Losses,” Recomb 98.Google Scholar
- 12.R. D. M. Page. “Maps between trees and cladistic analysis of historical associations among genes, organisms, and areas,” Syst. Biol. 43 (1994), 58–77.Google Scholar
- 13.D. L. Swofford. “When are phylogeny estimates from molecular and morphological data incongruent?” in Phylogenetic analysis of DNA sequences, Oxford Univ. Press (1991), pp. 295–333Google Scholar