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Volumn 18, Issue 9, 2011, Pages 1131-1139

Fast and accurate phylogenetic reconstruction from high-resolution whole-genome data and a novel robustness estimator

Author keywords

Algorithms; bootstrapping; combinatorial optimization; computational molecular biology; genomic rearrangements; phylogenetic analyses

Indexed keywords

ANIMAL; BIOLOGICAL MODEL; COMPUTER PROGRAM; COMPUTER SIMULATION; CONFERENCE PAPER; DNA SEQUENCE; GENE REARRANGEMENT; GENOME; HUMAN; METHODOLOGY; MOLECULAR EVOLUTION; MUTATION; NONPARAMETRIC TEST; PHYLOGENY; RECEIVER OPERATING CHARACTERISTIC; STATISTICAL ANALYSIS; SYNTENY;

EID: 80052624718     PISSN: 10665277     EISSN: None     Source Type: Journal    
DOI: 10.1089/cmb.2011.0114     Document Type: Conference Paper
Times cited : (14)

References (33)
  • 1
    • 66049158304 scopus 로고    scopus 로고
    • Breakpoint graphs and ancestral genome reconstructions
    • Alekseyev, M., and Pevzner, P. 2009. Breakpoint graphs and ancestral genome reconstructions. Genome Res. 19, 943-957.
    • (2009) Genome Res. , vol.19 , pp. 943-957
    • Alekseyev, M.1    Pevzner, P.2
  • 2
    • 0141609704 scopus 로고    scopus 로고
    • A new phylogenetic marker, apolipoprotein B, provides compelling evidence for eutherian relationships
    • DOI 10.1016/S1055-7903(03)00118-0
    • Amrine-Madsen, H., Koepfli, K.-P., Wayne, R., et al. 2003. A new phylogenetic marker, apolipoprotein b, provides compelling evidence for eutherian relationships. Mol. Phylogenet Evol. 28, 225-240. (Pubitemid 37446824)
    • (2003) Molecular Phylogenetics and Evolution , vol.28 , Issue.2 , pp. 225-240
    • Amrine-Madsen, H.1    Koepfli, K.-P.2    Wayne, R.K.3    Springer, M.S.4
  • 4
    • 0002163159 scopus 로고    scopus 로고
    • Breakpoint phylogenies
    • In Miyano, S., and Takagi, T., eds. University Academy Press, Tokyo
    • Blanchette, M., Bourque, G., and Sankoff, D. 1997. Breakpoint phylogenies, 25-34. In Miyano, S., and Takagi, T., eds., Genome Informatics, University Academy Press, Tokyo.
    • (1997) Genome Informatics , pp. 25-34
    • Blanchette, M.1    Bourque, G.2    Sankoff, D.3
  • 5
    • 0036143403 scopus 로고    scopus 로고
    • Genome-scale evolution: Reconstructing gene orders in the ancestral species
    • Bourque, G., and Pevzner, P. 2002. Genome-scale evolution: reconstructing gene orders in the ancestral species. Genome Res. 12, 26-36. (Pubitemid 34065587)
    • (2002) Genome Research , vol.12 , Issue.1 , pp. 26-36
    • Bourque, G.1    Pevzner, P.A.2
  • 7
    • 0023099491 scopus 로고
    • Computational complexity of inferring phylogenies from chromosome inversion data
    • DOI 10.1016/S0022-5193(87)80263-1
    • Day, W., and Sankoff, D. 1987. The computational complexity of inferring phylogenies from chromosome inversion data. J. Theor. Biol. 127, 213-218. (Pubitemid 17004339)
    • (1987) Journal of Theoretical Biology , vol.124 , Issue.2 , pp. 213-218
    • Day, W.H.E.1    Sankoff, D.2
  • 8
    • 0000461280 scopus 로고
    • Confidence limits on phylogenies: An approach using the bootstrap
    • Felsenstein, J. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39, 783-791.
    • (1985) Evolution , vol.39 , pp. 783-791
    • Felsenstein, J.1
  • 9
    • 12044259827 scopus 로고
    • Is there something wrong with the bootstrap on phylogenies? A reply to Hillis and Bull
    • Felsenstein, J., and Kishino, H. 1993. Is there something wrong with the bootstrap on phylogenies? A reply to Hillis and Bull. Syst. Biol. 42, 193-200.
    • (1993) Syst. Biol. , vol.42 , pp. 193-200
    • Felsenstein, J.1    Kishino, H.2
  • 11
    • 2642613543 scopus 로고
    • Assessing molecular phylogenies
    • Hillis, D., and Huelsenbeck, J. 1995. Assessing molecular phylogenies. Science 267, 255-256.
    • (1995) Science , vol.267 , pp. 255-256
    • Hillis, D.1    Huelsenbeck, J.2
  • 12
    • 34547753508 scopus 로고    scopus 로고
    • Rates of genome evolution and branching order from whole genome analysis
    • DOI 10.1093/molbev/msm094
    • Huttley, G., Wakefield, M., and Easteal, S. 2007. Rates of genome evolution and branching order from whole-genome analysis. Mol. Biol. Evol. 24, 1722-1730. (Pubitemid 47236694)
    • (2007) Molecular Biology and Evolution , vol.24 , Issue.8 , pp. 1722-1730
    • Huttley, G.A.1    Wakefield, M.J.2    Easteal, S.3
  • 13
    • 46249101804 scopus 로고    scopus 로고
    • Estimating true evolutionary distances under the DCJ model
    • DOI 10.1093/bioinformatics/btn148
    • Lin, Y., and Moret, B. 2008. Estimating true evolutionary distances under the DCJ model. Bioinformatics 24, i114-i122. (Pubitemid 351911664)
    • (2008) Bioinformatics , vol.24 , Issue.13
    • Lin, Y.1    Moret, B.M.E.2
  • 14
    • 75149182864 scopus 로고    scopus 로고
    • Estimating true evolutionary distances under rearrangements, duplications, and losses
    • Lin, Y., Rajan, V., Swenson, K., et al. 2010. Estimating true evolutionary distances under rearrangements, duplications, and losses. BMCBioinform. 11, S54.
    • (2010) BMCBioinform. , vol.11
    • Lin, Y.1    Rajan, V.2    Swenson, K.3
  • 16
    • 23844520968 scopus 로고    scopus 로고
    • Steps toward accurate reconstructions of phylogenies from gene-order data
    • DOI 10.1016/S0022-0000(02)00007-7, PII S0022000002000077
    • Moret, B., Tang, J., Wang, L.-S., et al. 2002. Steps toward accurate reconstructions of phylogenies from gene-order data. J. Comput. Syst. Sci. 65, 508-525. (Pubitemid 41161953)
    • (2003) Journal of Computer and System Sciences , vol.65 , Issue.3 , pp. 508-525
    • Moret, B.M.E.1    Tang, J.2    Wang, L.-S.3    Warnow, T.4
  • 17
    • 0035234694 scopus 로고    scopus 로고
    • A new implementation and detailed study of breakpoint analysis
    • Moret, B., Wyman, S., Bader, D., et al. 2001. A new implementation and detailed study of breakpoint analysis. Proc. 6th Pac. Symp. Biocomput. 583-594.
    • (2001) Proc. 6th Pac. Symp. Biocomput. , pp. 583-594
    • Moret, B.1    Wyman, S.2    Bader, D.3
  • 19
    • 85036788482 scopus 로고    scopus 로고
    • A language and environment for statistical computing
    • R Development Core Team, 2009. R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna.
    • (2009) R Foundation for Statistical Computing, Vienna
  • 20
    • 0019424782 scopus 로고
    • Comparison of phylogenetic trees
    • DOI 10.1016/0025-5564(81)90043-2
    • Robinson, D., and Foulds, L. 1981. Comparison of phylogenetic trees. Math. Biosci. 53, 131-147. (Pubitemid 11129084)
    • (1981) Mathematical Biosciences , vol.53 , Issue.1-2 , pp. 131-147
    • Robinson, D.F.1    Foulds, L.R.2
  • 21
    • 0033793019 scopus 로고    scopus 로고
    • Rare genomic changes as a tool for phylogenetics
    • Rokas, A., and Holland, P. 2000. Rare genomic changes as a tool for phylogenetics. Trends Ecol. Evol. 15, 454-459.
    • (2000) Trends Ecol. Evol. , vol.15 , pp. 454-459
    • Rokas, A.1    Holland, P.2
  • 22
    • 0023375195 scopus 로고
    • The neighbor-joining method: A new method for reconstructing phylogenetic trees
    • Saitou, N., and Nei, M. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4, 406-425.
    • (1987) Mol. Biol. Evol. , vol.4 , pp. 406-425
    • Saitou, N.1    Nei, M.2
  • 23
    • 77950533243 scopus 로고    scopus 로고
    • Using jackknife to assess the quality of gene order phylogenies
    • Shi, J., Zhang, Y., Luo, H., et al. 2010. Using jackknife to assess the quality of gene order phylogenies. BMC Bioinform. 11, 168.
    • (2010) BMC Bioinform. , vol.11 , pp. 168
    • Shi, J.1    Zhang, Y.2    Luo, H.3
  • 24
    • 0347532847 scopus 로고    scopus 로고
    • Applying the bootstrap in phylogeny reconstruction
    • DOI 10.1214/ss/1063994980
    • Soltis, P., and Soltis, D. 2003. Applying the bootstrap in phylogeny reconstruction. Statist. Sci. 18, 256-267. (Pubitemid 37545098)
    • (2003) Statistical Science , vol.18 , Issue.2 , pp. 256-267
    • Soltis, P.S.1    Soltis, D.E.2
  • 25
    • 0001637701 scopus 로고
    • A crossover reducer in Drosophila melanogaster due to inversion of a section of the third chromosome
    • Sturtevant, A. 1926. A crossover reducer in Drosophila melanogaster due to inversion of a section of the third chromosome. Biol. Zent. Bl. 46, 697-702.
    • (1926) Biol. Zent. Bl. , vol.46 , pp. 697-702
    • Sturtevant, A.1
  • 26
    • 0000309645 scopus 로고
    • Inversions in the third chromosome of wild races of drosophila pseu-doobscura and their use in the study of the history of the species
    • Sturtevant, A., and Dobzhansky, T. 1936. Inversions in the third chromosome of wild races of drosophila pseu-doobscura and their use in the study of the history of the species. Proc. Natl. Acad. Sci. USA 22, 448-450.
    • (1936) Proc. Natl. Acad. Sci. USA , vol.22 , pp. 448-450
    • Sturtevant, A.1    Dobzhansky, T.2
  • 27
    • 0001336205 scopus 로고    scopus 로고
    • Phylogenetic inference
    • In Hillis D., Mable, B., and Moritz C., eds. Sunderland, MA
    • Swofford, D., Olsen, G., Waddell, P., et al. 1996. Phylogenetic inference, 407-514. In Hillis, D., Mable, B., and Moritz, C., eds., Molecular Systematics, Sinauer Assoc., Sunderland, MA.
    • (1996) Molecular Systematics, Sinauer Assoc , pp. 407-514
    • Swofford, D.1    Olsen, G.2    Waddell, P.3
  • 28
    • 0345225320 scopus 로고    scopus 로고
    • Scaling up accurate phylogenetic reconstruction from gene-order data
    • Tang, J., and Moret, B. 2003. Scaling up accurate phylogenetic reconstruction from gene-order data. Bioinformatics 19, i305-i312.
    • (2003) Bioinformatics , vol.19
    • Tang, J.1    Moret, B.2
  • 30
    • 0008745750 scopus 로고    scopus 로고
    • Estimating true evolutionary distances between genomes
    • Wang, L.-S., and Warnow, T. 2001. Estimating true evolutionary distances between genomes. Lect. Notes Comput. Sci. 2149, 176-190.
    • (2001) Lect. Notes Comput. Sci. , vol.2149 , pp. 176-190
    • Wang, L.-S.1    Warnow, T.2
  • 32
    • 24044535485 scopus 로고    scopus 로고
    • Efficient sorting of genomic permutations by translocation, inversion and block interchange
    • DOI 10.1093/bioinformatics/bti535
    • Yancopoulos, S., Attie, O., and Friedberg, R. 2005. Efficient sorting of genomic permutations by translocation, inversion and block interchange. Bioinformatics 21, 3340-3346. (Pubitemid 41222437)
    • (2005) Bioinformatics , vol.21 , Issue.16 , pp. 3340-3346
    • Yancopoulos, S.1    Attie, O.2    Friedberg, R.3
  • 33
    • 0036699481 scopus 로고    scopus 로고
    • Increased taxon sampling greatly reduces phylogenetic error
    • DOI 10.1080/10635150290102339
    • Zwickl, D., and Hillis, D. 2002. Increased taxon sampling greatly reduces phylogenetic error. Syst. Biol. 51, 588-598. (Pubitemid 35180690)
    • (2002) Systematic Biology , vol.51 , Issue.4 , pp. 588-598
    • Zwickl, D.J.1    Hillis, D.M.2


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