메뉴 건너뛰기




Volumn 22, Issue 3, 2005, Pages 792-802

Comparison of the accuracies of several phylogenetic methods using protein and DNA sequences

Author keywords

Alignment; Branch lengths; Indels; Method comparison; Simulation; Topology

Indexed keywords

DNA; PROTEIN;

EID: 14544277657     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/molbev/msi066     Document Type: Article
Times cited : (162)

References (31)
  • 1
    • 0037008841 scopus 로고    scopus 로고
    • Phylogenetic analysis shows that the oxa β-lactamase genes have been on plasmids for millions of years
    • Barlow, M., and B. G. Hall. 2002. Phylogenetic analysis shows that the oxa β-lactamase genes have been on plasmids for millions of years. J. Mol. Evol. 55:314-321.
    • (2002) J. Mol. Evol. , vol.55 , pp. 314-321
    • Barlow, M.1    Hall, B.G.2
  • 3
    • 0019858614 scopus 로고
    • Similar amino acid sequences: Chance or common ancestry?
    • Doolittle, R. F. 1981. Similar amino acid sequences: chance or common ancestry? Science 214:149-159.
    • (1981) Science , vol.214 , pp. 149-159
    • Doolittle, R.F.1
  • 4
    • 0019797407 scopus 로고
    • Evolutionary trees from DNA sequences: A maximum likelihood approach
    • Felsenstein, J. 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol. 17:368-376.
    • (1981) J. Mol. Evol. , vol.17 , pp. 368-376
    • Felsenstein, J.1
  • 5
    • 0022438882 scopus 로고
    • Mechanisms of spontaneous mutagenesis: Clues from altered mutational specificity in DNA repair-defective strains
    • D. M. Shankel, P. E. Hartman, T. Kada, and A. Hollender, eds. Plenum Press, New York
    • Glickman, B. W., P. A. Burns, and D. F. Fix. 1986. Mechanisms of spontaneous mutagenesis: clues from altered mutational specificity in DNA repair-defective strains. Pp. 259-281 in D. M. Shankel, P. E. Hartman, T. Kada, and A. Hollender, eds. Antimutagenesis and anticarcinogenesis mechanisms. Plenum Press, New York.
    • (1986) Antimutagenesis and Anticarcinogenesis Mechanisms , pp. 259-281
    • Glickman, B.W.1    Burns, P.A.2    Fix, D.F.3
  • 6
    • 0033061057 scopus 로고    scopus 로고
    • The spectra of spontaneous growth-dependent and adaptive mutations in ebgR
    • Hall, B. G. 1999. The spectra of spontaneous growth-dependent and adaptive mutations in ebgR. J. Bacteriol. 181:1149-1155.
    • (1999) J. Bacteriol. , vol.181 , pp. 1149-1155
    • Hall, B.G.1
  • 7
    • 14544307740 scopus 로고    scopus 로고
    • Macintosh, Windows, Unix Distributed by the author., Bellingham, WA
    • Hall, B. G. 2004a. CodonAlign. Macintosh, Windows, Unix Distributed by the author., Bellingham, WA.
    • (2004) CodonAlign
    • Hall, B.G.1
  • 9
    • 14544276944 scopus 로고    scopus 로고
    • Macintosh Distributed by the author, Bellingham, WA
    • Hall, B. G. 2004c. TuneClustalX. Macintosh Distributed by the author, Bellingham, WA.
    • (2004) TuneClustalX
    • Hall, B.G.1
  • 10
    • 14544302073 scopus 로고    scopus 로고
    • Macintosh Distributed by the author, Bellingham, WA
    • Hall, B. G. 2004d. CompareTrees. Macintosh Distributed by the author, Bellingham, WA.
    • (2004) CompareTrees
    • Hall, B.G.1
  • 11
    • 14544288963 scopus 로고    scopus 로고
    • Macintosh Distributed by the author, Bellingham, WA
    • Hall, B. G. 2004e. EvolveAGene. Macintosh Distributed by the author, Bellingham, WA.
    • (2004) EvolveAGene
    • Hall, B.G.1
  • 12
    • 2942562249 scopus 로고    scopus 로고
    • Evolution of the serine β-lactamases: Past, present and future
    • Hall, B. G., and M. Barlow. 2004. Evolution of the serine β-lactamases: past, present and future. Drug Resist. Update 7:111-123.
    • (2004) Drug Resist. Update , vol.7 , pp. 111-123
    • Hall, B.G.1    Barlow, M.2
  • 13
    • 3042808576 scopus 로고    scopus 로고
    • Independent origins of the Subgroup (B1+B2) and the Subgroup B3 metallo-β-lactamases
    • Hall, B. G., S. J. Salipante, and M. Barlow. 2004. Independent origins of the Subgroup (B1+B2) and the Subgroup B3 metallo-β-lactamases. J. Mol. Evol. 59:132-140.
    • (2004) J. Mol. Evol. , vol.59 , pp. 132-140
    • Hall, B.G.1    Salipante, S.J.2    Barlow, M.3
  • 14
    • 0022376704 scopus 로고
    • Dating of the human-ape splitting by a molecular clock of mitochondrial DNA
    • Hasegawa, M., H. Kishino, and T. Yano. 1985. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J. Mol. Evol. 22:160-174.
    • (1985) J. Mol. Evol. , vol.22 , pp. 160-174
    • Hasegawa, M.1    Kishino, H.2    Yano, T.3
  • 15
  • 16
    • 0028362880 scopus 로고
    • Application and accuracy of molecular phytogenies
    • Hillis, D. M., J. P. Huelsenbeck, and C. W. Cunningham. 1994. Application and accuracy of molecular phytogenies. Science 264:671-677.
    • (1994) Science , vol.264 , pp. 671-677
    • Hillis, D.M.1    Huelsenbeck, J.P.2    Cunningham, C.W.3
  • 17
    • 0034849408 scopus 로고    scopus 로고
    • MrBayes: Bayesian inference of phytogeny
    • Huelsenbeck, J. P., and F. Ronquist. 2001. MrBayes: Bayesian inference of phytogeny. Bioinformatics 17:754-755.
    • (2001) Bioinformatics , vol.17 , pp. 754-755
    • Huelsenbeck, J.P.1    Ronquist, F.2
  • 18
    • 0000732090 scopus 로고
    • Evolution of protein molecules
    • H. N. Munro, ed. Academic Press, New York
    • Jukes, T. H., and C. R. Cantor. 1969. Evolution of protein molecules. Pp. 21-32 in H. N. Munro, ed. Mammalian protein metabolism. Academic Press, New York.
    • (1969) Mammalian Protein Metabolism , pp. 21-32
    • Jukes, T.H.1    Cantor, C.R.2
  • 19
    • 0019296687 scopus 로고
    • A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences
    • Kimura, M. 1980. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 16:111-120.
    • (1980) J. Mol. Evol. , vol.16 , pp. 111-120
    • Kimura, M.1
  • 20
    • 0028177080 scopus 로고
    • A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates
    • Kuhner, M. K., and J. Felsenstein. 1994. A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates. Mol. Biol. Evol. 11:459-468.
    • (1994) Mol. Biol. Evol. , vol.11 , pp. 459-468
    • Kuhner, M.K.1    Felsenstein, J.2
  • 21
    • 0003421005 scopus 로고    scopus 로고
    • Sinauer Associates, Sunderland, Mass.
    • Li, W.-H. 1997. Molecular evolution. Sinauer Associates, Sunderland, Mass.
    • (1997) Molecular Evolution
    • Li, W.-H.1
  • 23
    • 0000329594 scopus 로고
    • Relative efficiencies of the Fitch-Margoliash, maximum parsimony, maximum-likelihood, minimum-evolution, and Neighbor-Joining methods of phylogenetic tree construction in obtaining the correct tree
    • Saitou, N., and T. Imanishi. 1989. Relative efficiencies of the Fitch-Margoliash, maximum parsimony, maximum-likelihood, minimum-evolution, and Neighbor-Joining methods of phylogenetic tree construction in obtaining the correct tree. Mol. Biol. Evol. 6:514-525.
    • (1989) Mol. Biol. Evol. , vol.6 , pp. 514-525
    • Saitou, N.1    Imanishi, T.2
  • 24
    • 0022446219 scopus 로고
    • Mechanisms of spontaneous mutagenesis: An analysis of the spectrum of spontaneous mutation in the Escherichia coli lacI gene
    • Schaaper, R. M., B. N. Danforth, and B. W. Glickman. 1986. Mechanisms of spontaneous mutagenesis: an analysis of the spectrum of spontaneous mutation in the Escherichia coli lacI gene. J. Mol. Biol. 189:273-284.
    • (1986) J. Mol. Biol. , vol.189 , pp. 273-284
    • Schaaper, R.M.1    Danforth, B.N.2    Glickman, B.W.3
  • 25
    • 0025953766 scopus 로고
    • Spontaneous mutations in the Escherichia coli lacI gene
    • Schaaper, R. M., and R. L. Dunn. 1991. Spontaneous mutations in the Escherichia coli lacI gene. Genetics 129:317-326.
    • (1991) Genetics , vol.129 , pp. 317-326
    • Schaaper, R.M.1    Dunn, R.L.2
  • 26
    • 0031857684 scopus 로고    scopus 로고
    • ROSE: Generating sequence families
    • Stoye, J., D. Evers, and F. Meyer. 1998. ROSE: generating sequence families. Bioinformatics 14:157-163.
    • (1998) Bioinformatics , vol.14 , pp. 157-163
    • Stoye, J.1    Evers, D.2    Meyer, F.3
  • 28
    • 0031574072 scopus 로고    scopus 로고
    • The ClustalX windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools
    • Thompson, J. D., T. J. Gibson, F. Plewniak, F. Jeanmougin, and D. G. Higgins. 1997. The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25:4876-4882.
    • (1997) Nucleic Acids Res. , vol.25 , pp. 4876-4882
    • Thompson, J.D.1    Gibson, T.J.2    Plewniak, F.3    Jeanmougin, F.4    Higgins, D.G.5
  • 29
    • 0033168097 scopus 로고    scopus 로고
    • A comprehensive comparison of multiple sequence alignment programs
    • Thompson, J. D., F. Plewniak, and O. Poch. 1999. A comprehensive comparison of multiple sequence alignment programs. Nucleic Acids Res. 27:2682-2690.
    • (1999) Nucleic Acids Res. , vol.27 , pp. 2682-2690
    • Thompson, J.D.1    Plewniak, F.2    Poch, O.3
  • 30
    • 0030683599 scopus 로고    scopus 로고
    • PAML: A program package for phylogenetic analysis by maximum likelihood
    • Yang, Z. 1997. PAML: a program package for phylogenetic analysis by maximum likelihood. Comput. Appl. Biosci. 13:555-556.
    • (1997) Comput. Appl. Biosci. , vol.13 , pp. 555-556
    • Yang, Z.1
  • 31
    • 0034097381 scopus 로고    scopus 로고
    • Cbdon-substitution models for heterogeneous selection pressure at amino acid sites
    • Yang, Z., R. Nielsen, N. Goldman, and A. M. Pedersen. 2000. Cbdon-substitution models for heterogeneous selection pressure at amino acid sites. Genetics 155:431-449.
    • (2000) Genetics , vol.155 , pp. 431-449
    • Yang, Z.1    Nielsen, R.2    Goldman, N.3    Pedersen, A.M.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.