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Volumn 4983 LNBI, Issue , 2008, Pages 14-25

The gene-duplication problem: Near-linear time algorithms for NNI based local searches

Author keywords

[No Author keywords available]

Indexed keywords

BIOCOMMUNICATIONS; BIOINFORMATICS; CHLORINE COMPOUNDS; HEURISTIC PROGRAMMING; INFORMATION SCIENCE; NUCLEAR PROPULSION; TREES (MATHEMATICS);

EID: 49949102302     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-540-79450-9_3     Document Type: Conference Paper
Times cited : (8)

References (29)
  • 1
    • 0347512294 scopus 로고    scopus 로고
    • Subtree transfer operations and their induced metrics on evolutionary trees
    • Allen, B.L., Steel, M.: Subtree transfer operations and their induced metrics on evolutionary trees. Annals of Combinatorics 5, 1-13 (2001)
    • (2001) Annals of Combinatorics , vol.5 , pp. 1-13
    • Allen, B.L.1    Steel, M.2
  • 2
    • 34547428923 scopus 로고    scopus 로고
    • Bansal, M.S., Burleigh, J.G., Eulenstein, O., Wehe, A.: Heuristics for the gene-duplication problem: A Θ(n) speed-up for the local search. In: Speed, T., Huang, H. (eds.) RECOMB 2007. LNCS (LNBI), 4453, pp. 238-252. Springer, Heidelberg (2007)
    • Bansal, M.S., Burleigh, J.G., Eulenstein, O., Wehe, A.: Heuristics for the gene-duplication problem: A Θ(n) speed-up for the local search. In: Speed, T., Huang, H. (eds.) RECOMB 2007. LNCS (LNBI), vol. 4453, pp. 238-252. Springer, Heidelberg (2007)
  • 3
    • 37249081512 scopus 로고    scopus 로고
    • 2/logn) speed-up of TBR heuristics for the geneduplication problem. In: Giancarlo, R., Hannenhalli, S. (eds.) WABI 2007. LNCS (LNBI), 4645, pp. 124-135. Springer, Heidelberg (2007)
    • 2/logn) speed-up of TBR heuristics for the geneduplication problem. In: Giancarlo, R., Hannenhalli, S. (eds.) WABI 2007. LNCS (LNBI), vol. 4645, pp. 124-135. Springer, Heidelberg (2007)
  • 4
    • 84896788505 scopus 로고    scopus 로고
    • The LCA problem revisited
    • Gonnet, G.H, Viola, A, eds, LATIN 2000, Springer, Heidelberg
    • Bender, M.A., Farach-Colton, M.: The LCA problem revisited. In: Gonnet, G.H., Viola, A. (eds.) LATIN 2000. LNCS, vol. 1776, pp. 88-94. Springer, Heidelberg (2000)
    • (2000) LNCS , vol.1776 , pp. 88-94
    • Bender, M.A.1    Farach-Colton, M.2
  • 5
    • 27844468683 scopus 로고    scopus 로고
    • Reconciling a gene tree to a species tree under the duplication cost model
    • Bonizzoni, P., Vedova, G.D., Dondi, R.: Reconciling a gene tree to a species tree under the duplication cost model. Theor. Comput. Sci. 347(1-2), 36-53 (2005)
    • (2005) Theor. Comput. Sci , vol.347 , Issue.1-2 , pp. 36-53
    • Bonizzoni, P.1    Vedova, G.D.2    Dondi, R.3
  • 6
    • 13844266486 scopus 로고    scopus 로고
    • On the computational complexity of the rooted subtree prune and regraft distance
    • Bordewich, M., Semple, C.: On the computational complexity of the rooted subtree prune and regraft distance. Annals of Combinatorics 8,409-423 (2004)
    • (2004) Annals of Combinatorics , vol.8 , pp. 409-423
    • Bordewich, M.1    Semple, C.2
  • 7
    • 0033692378 scopus 로고    scopus 로고
    • Notung: A program for dating gene duplications and optimizing gene family trees
    • Chen, K., Durand, D., Farach-Colton, M.: Notung: a program for dating gene duplications and optimizing gene family trees. Journal of Computational Biology 7, 429-447 (2000)
    • (2000) Journal of Computational Biology , vol.7 , pp. 429-447
    • Chen, K.1    Durand, D.2    Farach-Colton, M.3
  • 8
    • 19944410649 scopus 로고    scopus 로고
    • Tangled tales from multiple markers: Reconciling conflict between phylogenies to build molecular supertrees
    • Springer, Heidelberg
    • Cotton, J.A., Page, R.D.M.: Tangled tales from multiple markers: reconciling conflict between phylogenies to build molecular supertrees. In: Phylogenetic Supertrees: Combining Information to Reveal the Tree of Life, pp. 107-125. Springer, Heidelberg (2004)
    • (2004) Phylogenetic Supertrees: Combining Information to Reveal the Tree of Life , pp. 107-125
    • Cotton, J.A.1    Page, R.D.M.2
  • 10
    • 84896746389 scopus 로고    scopus 로고
    • Fellows, M., Hallett, M., Korostensky, C., Stege, U.: Analogs and duals of the mast problem for sequences and trees. In: Bilardi, G., Pietracaprina, A., Italiano, G.F., Pucci, G. (eds.) ESA 1998. LNCS, 1461, pp. 103-114. Springer, Heidelberg (1998)
    • Fellows, M., Hallett, M., Korostensky, C., Stege, U.: Analogs and duals of the mast problem for sequences and trees. In: Bilardi, G., Pietracaprina, A., Italiano, G.F., Pucci, G. (eds.) ESA 1998. LNCS, vol. 1461, pp. 103-114. Springer, Heidelberg (1998)
  • 11
    • 35248894002 scopus 로고    scopus 로고
    • Ganapathy, G., Ramachandran, V., Warnow, T.: Better hill-climbing searches for parsimony. In: Benson, G., Page, R.D.M. (eds.) WABI 2003. LNCS (LNBI), 2812, pp. 245-258. Springer, Heidelberg (2003)
    • Ganapathy, G., Ramachandran, V., Warnow, T.: Better hill-climbing searches for parsimony. In: Benson, G., Page, R.D.M. (eds.) WABI 2003. LNCS (LNBI), vol. 2812, pp. 245-258. Springer, Heidelberg (2003)
  • 13
    • 0000365320 scopus 로고
    • Fitting the gene lineage into its species lineage. a parsimony strategy illustrated by cladograms constructed from globin sequences
    • Goodman, M., Czelusniak, J., Moore, G.W., Romero-Herrera, A.E., Matsuda, G.: Fitting the gene lineage into its species lineage. a parsimony strategy illustrated by cladograms constructed from globin sequences. Systematic Zoology 28, 132-163 (1979)
    • (1979) Systematic Zoology , vol.28 , pp. 132-163
    • Goodman, M.1    Czelusniak, J.2    Moore, G.W.3    Romero-Herrera, A.E.4    Matsuda, G.5
  • 14
    • 26444580983 scopus 로고    scopus 로고
    • Górecki, P., Tiuryn, J.: On the structure of reconciliations. In: Lagergren, J. (ed.) RECOMBWS 2004. LNCS (LNBI), 3388, pp. 42-54. Springer, Heidelberg (2005)
    • Górecki, P., Tiuryn, J.: On the structure of reconciliations. In: Lagergren, J. (ed.) RECOMBWS 2004. LNCS (LNBI), vol. 3388, pp. 42-54. Springer, Heidelberg (2005)
  • 16
    • 0033723163 scopus 로고    scopus 로고
    • New algorithms for the duplication-loss model
    • Hallett, M.T., Lagergren, J.: New algorithms for the duplication-loss model. In: RECOMB, pp. 138-146 (2000)
    • (2000) RECOMB , pp. 138-146
    • Hallett, M.T.1    Lagergren, J.2
  • 17
    • 0034938644 scopus 로고    scopus 로고
    • From gene trees to species trees
    • Ma, B., Li, M., Zhang, L.: From gene trees to species trees. SIAM J. Comput. 30(3), 729-752 (2000)
    • (2000) SIAM J. Comput , vol.30 , Issue.3 , pp. 729-752
    • Ma, B.1    Li, M.2    Zhang, L.3
  • 18
    • 0029448349 scopus 로고
    • A biology consistent model for comparing molecular phylogenies
    • Mirkin, B., Muchnik, I., Smith, T.F.: A biology consistent model for comparing molecular phylogenies. Journal of Computational Biology 2(4), 493-507 (1995)
    • (1995) Journal of Computational Biology , vol.2 , Issue.4 , pp. 493-507
    • Mirkin, B.1    Muchnik, I.2    Smith, T.F.3
  • 19
    • 12044253257 scopus 로고
    • Maps between trees and cladistic analysis of historical associations among genes, organisms, and areas
    • Page, R.D.M.: Maps between trees and cladistic analysis of historical associations among genes, organisms, and areas. Systematic Biology 43(1), 58-77 (1994)
    • (1994) Systematic Biology , vol.43 , Issue.1 , pp. 58-77
    • Page, R.D.M.1
  • 20
    • 0031774059 scopus 로고    scopus 로고
    • GeneTree: Comparing gene and species phylogenies using reconciled trees
    • Page, R.D.M.: GeneTree: comparing gene and species phylogenies using reconciled trees. Bioinformatics 14(9), 819-820 (1998)
    • (1998) Bioinformatics , vol.14 , Issue.9 , pp. 819-820
    • Page, R.D.M.1
  • 21
    • 0033936591 scopus 로고    scopus 로고
    • Extracting species trees from complex gene trees: Reconciled trees and vertebrate phylogeny
    • Page, R.D.M.: Extracting species trees from complex gene trees: reconciled trees and vertebrate phylogeny. Molecular Phylogenetics and Evolution 14, 89-106 (2000)
    • (2000) Molecular Phylogenetics and Evolution , vol.14 , pp. 89-106
    • Page, R.D.M.1
  • 22
    • 0031110886 scopus 로고    scopus 로고
    • From gene to organismal phylogeny: Reconciled trees and the gene tree/species tree problem
    • Page, R.D.M., Charleston, M.A.: From gene to organismal phylogeny: reconciled trees and the gene tree/species tree problem. Molec. Phyl. and Evol. 7, 231-240 (1997)
    • (1997) Molec. Phyl. and Evol , vol.7 , pp. 231-240
    • Page, R.D.M.1    Charleston, M.A.2
  • 23
    • 0036365666 scopus 로고    scopus 로고
    • Vertebrate phylogenomics: Reconciled trees and gene duplications
    • Page, R.D.M., Cotton, J.: Vertebrate phylogenomics: reconciled trees and gene duplications. In: Pacific Symposium on Biocomputing, pp. 536-547 (2002)
    • (2002) Pacific Symposium on Biocomputing , pp. 536-547
    • Page, R.D.M.1    Cotton, J.2
  • 25
    • 34248217100 scopus 로고    scopus 로고
    • Inferring angiosperm phylogeny from EST data with widespread gene duplication
    • Sanderson, M.J., McMahon, M.M.: Inferring angiosperm phylogeny from EST data with widespread gene duplication. BMC Evolutionary Biology 7 (suppl. 1), 3 (2007)
    • (2007) BMC Evolutionary Biology , vol.7 , Issue.SUPPL. 1 , pp. 3
    • Sanderson, M.J.1    McMahon, M.M.2
  • 27
    • 0031296691 scopus 로고    scopus 로고
    • Inferring species trees from gene trees: A phylogenetic analysis of the elapidae (serpentes) based on the amino acid sequences of venom proteins
    • Slowinski, J.B., Knight, A., Rooney, A.P.: Inferring species trees from gene trees: A phylogenetic analysis of the elapidae (serpentes) based on the amino acid sequences of venom proteins. Molecular Phylogenetics and Evolution 8, 349-362 (1997)
    • (1997) Molecular Phylogenetics and Evolution , vol.8 , pp. 349-362
    • Slowinski, J.B.1    Knight, A.2    Rooney, A.P.3
  • 28
    • 84948965737 scopus 로고    scopus 로고
    • Stege, U.: Gene trees and species trees: The gene-duplication problem in fixed-parameter tractable. In: WADS, pp. 288-293 (1999)
    • Stege, U.: Gene trees and species trees: The gene-duplication problem in fixed-parameter tractable. In: WADS, pp. 288-293 (1999)
  • 29
    • 0030762443 scopus 로고    scopus 로고
    • On a Mirkin-Muchnik-Smith conjecture for comparing molecular phylogenies
    • Zhang, L.: On a Mirkin-Muchnik-Smith conjecture for comparing molecular phylogenies. Journal of Computational Biology 4(2), 177-187 (1997)
    • (1997) Journal of Computational Biology , vol.4 , Issue.2 , pp. 177-187
    • Zhang, L.1


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