Abstract
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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References
S. Benner and A. Ellington. Evolution and Structural Theory. The frontier between chemistry and biochemistry. Bioorg. Chem. Frontiers 1 (1990), 1–70.
R. G. Downey and M. R. Fellows. Parameterized Complexity, Springer, 1998.
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.
R. G. Downey, M. R. Fellows, and U. Stege. Computational Tractability: The View From Mars, to appear in the Bulletin of the EATCS.
J. Felsenstein. Phylogenies from Molecular Sequences: Inference and Reliability. Annu. Rev. Genet. (1988), 22, 521–65.
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).
W. Fitch, E. Margoliash. “Construction of Phylogenetic Tree,” Sci. 155 (1967).
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.
R. Guigó, I. Muchnik, and T. F. Smith. “Reconstruction of Ancient Molecular Phylogeny,” Molec. Phylogenet. and Evol. (1996),6:2, 189–213.
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).
B. Ma, M. Li, and L. Zhang. “On Reconstructing Species Trees from Gene Trees in Term of Duplications and Losses,” Recomb 98.
R. D. M. Page. “Maps between trees and cladistic analysis of historical associations among genes, organisms, and areas,” Syst. Biol. 43 (1994), 58–77.
D. L. Swofford. “When are phylogeny estimates from molecular and morphological data incongruent?” in Phylogenetic analysis of DNA sequences, Oxford Univ. Press (1991), pp. 295–333
L. Zhang. “On a Mirkin-Muchnik-Smith Conjecture for Comparing Molecular Phylogenies,” Journal of Comp. Biol. (1997) 4:2, 177–187.
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© 1999 Springer-Verlag Berlin Heidelberg
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Stege, U. (1999). Gene Trees and Species Trees: The Gene-Duplication Problem is Fixed-Parameter Tractable. In: Dehne, F., Sack, JR., Gupta, A., Tamassia, R. (eds) Algorithms and Data Structures. WADS 1999. Lecture Notes in Computer Science, vol 1663. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-48447-7_29
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DOI: https://doi.org/10.1007/3-540-48447-7_29
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