메뉴 건너뛰기




Volumn 18, Issue 6, 2001, Pages 897-906

Selecting models of nucleotide substitution: An application to human immunodeficiency virus 1 (HIV-1)

Author keywords

Akaike information criterion; HIV 1; Likelihood ratio test; Model selection; Molecular clock

Indexed keywords

GAG PROTEIN; NUCLEOTIDE; POL PROTEIN; VIRUS ENVELOPE PROTEIN;

EID: 0034988391     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/oxfordjournals.molbev.a003890     Document Type: Article
Times cited : (129)

References (72)
  • 1
    • 0029039263 scopus 로고
    • Improved dating of the human/chimpanzee separation in the mitochondrial DNA tree: Heterogeneity among amino acid sites
    • (1995) J. Mol. Evol. , vol.40 , pp. 622-628
    • Adachi, J.1    Hasegawa, M.2
  • 4
    • 0028952146 scopus 로고
    • HIV population dynamics in vivo: Implications for genetic variation, pathogenesis, and therapy
    • (1995) Science , vol.267 , pp. 483-489
    • Coffin, J.M.1
  • 5
    • 84959798530 scopus 로고
    • Cases in which parsimony or compatibility methods will be positively misleading
    • (1978) Syst. Zool. , vol.27 , pp. 401-410
    • Felsenstein, J.1
  • 6
    • 0019797407 scopus 로고
    • Evolutionary trees from DNA sequences: A maximum likelihood approach
    • (1981) J. Mol. Evol. , vol.17 , pp. 368-376
  • 10
  • 12
    • 0025074891 scopus 로고
    • Mitochondrial DNA evolution in primates: Transition rate has been extremely low in the lemur
    • (1990) J. Mol. Evol. , vol.31 , pp. 113-121
    • Hasegawa, M.1
  • 13
    • 0025086910 scopus 로고
    • Phylogeny and molecular evolution in primates
    • (1990) Jpn. J. Genet. , vol.65 , pp. 243-266
  • 16
    • 0004902791 scopus 로고    scopus 로고
    • Phylogenetics and the study of HIV
    • K. A. Crandall, ed. The evolution of HIV. Johns Hopkins University Press, Baltimore, Md
    • (1999) , pp. 105-121
    • Hillis, D.M.1
  • 17
    • 0000704795 scopus 로고    scopus 로고
    • Applications of molecular systematics: The state of the field and a look to the future
    • D. M. Hillis, C. Moritz, and B. K. Mable, eds. Molecular systematics. Sinauer, Sunderland, Mass
    • (1996) , pp. 515-543
    • Hillis, D.M.1    Mable, B.K.2    Moritz, C.3
  • 18
    • 33645762226 scopus 로고
    • A sharper Bonferroni procedure for multiple tests of significance
    • (1988) Biometrika , vol.75 , pp. 800-802
    • Hochberg, Y.1
  • 19
    • 0002277392 scopus 로고    scopus 로고
    • The molecular population dynamics of HIV-1
    • K. A. Crandall, ed. The evolution of HIV. Johns Hopkins University Press, Baltimore, Md
    • (1999) , pp. 177-207
    • Holmes, E.C.1    Pybus, O.G.2    Harvey, E.H.3
  • 22
    • 0000732090 scopus 로고
    • Evolution of protein molecules
    • H. M. Munro, ed. Mammalian protein metabolism. Academic Press, N.Y.
    • (1969) , pp. 21-132
    • Jukes, T.H.1    Cantor, C.R.2
  • 25
    • 0019296687 scopus 로고
    • A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences
    • (1980) J. Mol. Evol. , vol.16 , pp. 111-120
    • Kimura, M.1
  • 26
    • 0001464973 scopus 로고
    • Estimation of evolutionary distances between homologous nucleotide sequences
    • (1981) Proc. Natl. Acad. Sci. USA , vol.78 , pp. 454-458
  • 31
    • 0001296312 scopus 로고    scopus 로고
    • The phylogenetics of known transmission histories
    • K. A. Crandall, ed. The evolution of HIV. Johns Hopkins University Press, Baltimore, Md
    • (1999) , pp. 315-345
    • Leitner, T.1    Fitch, W.M.2
  • 32
    • 0031010764 scopus 로고    scopus 로고
    • Tempo and mode of nucleotide substitutions in gag and env gene fragments in human immunodeficiency virus type 1 populations with a known transmission history
    • (1997) J. Virol. , vol.71 , pp. 4761-4770
    • Leitner, T.1    Kumar, S.2    Albert, J.3
  • 35
    • 0004854501 scopus 로고    scopus 로고
    • Modeling the molecular evolution of HIV sequences
    • K. A. Crandall, ed. The evolution of HIV. Johns Hopkins University Press, Baltimore, Md
    • (1999) , pp. 122-152
    • Muse, S.1
  • 36
    • 0028024626 scopus 로고
    • A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome
    • (1994) Mol. Biol. Evol. , vol.11 , pp. 715-724
    • Muse, S.V.1    Gaut, B.S.2
  • 41
    • 0001596085 scopus 로고
    • The role of models in reconstructing evolutionary trees
    • R. W. Scotland, D. J. Siebert, and D. M. Williams, eds. Models in phylogenetic reconstruction. Clarendon Press, Oxford, England
    • (1994) , pp. 211-230
    • Penny, D.1    Lockhart, P.J.2    Steel, M.A.3    Hendy, M.D.4
  • 43
    • 0035527410 scopus 로고    scopus 로고
    • Selecting the best-fit model of nucleotide substitution
    • in press
    • (2001) Syst. Biol.
  • 44
    • 85046529148 scopus 로고    scopus 로고
    • Simple (wrong) models for complex trees: Empirical bias
    • (2001) Mol. Biol. Evol. , vol.18 , pp. 271-275
  • 45
    • 0004911830 scopus 로고    scopus 로고
    • Phylogenetics of HIV
    • A. G. Rodrigo and G. H. J. Learn, eds. Computational and evolutionary analysis of HIV molecular sequences. Kluwer, Norwell, Mass
    • (2000) , pp. 121-160
    • Posada, D.1    Crandall, K.A.2    Hillis, D.M.3
  • 47
    • 0034044313 scopus 로고    scopus 로고
    • Estimating the rate of molecular evolution: Incorporating non-contemporaneous sequences into maximum likelihood phylogenies
    • (2000) Bioinformatics , vol.16 , pp. 395-399
  • 54
    • 0033805038 scopus 로고    scopus 로고
    • Recombination and the molecular clock
    • (2000) Mol. Biol. Evol. , vol.17 , pp. 1578-1579
  • 60
    • 0026711010 scopus 로고
    • Estimation of the number of nucleotide substitutions when there are strong transition-transversion and G+C content biases
    • (1992) Mol. Biol. Evol. , vol.9 , pp. 678-687
    • Tamura, K.1
  • 61
    • 0027157960 scopus 로고
    • Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees
    • (1993) Mol. Biol. Evol. , vol.10 , pp. 512-526
    • Tamura, K.1    Nei, M.2
  • 64
    • 0028064845 scopus 로고
    • Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods
    • (1994) J. Mol. Evol. , vol.39 , pp. 306-314
    • Yang, Z.1
  • 65
    • 0030451420 scopus 로고    scopus 로고
    • Among-site rate variation and its impact on phylogenetic analysis
    • (1996) Trends Ecol. Evol. , vol.11 , pp. 367-372
  • 66
    • 0030638573 scopus 로고    scopus 로고
    • How often do wrong models produce better phylogenies?
    • (1997) Mol. Biol. Evol. , vol.14 , pp. 105-108
  • 68
    • 0029469716 scopus 로고
    • Maximum likelihood trees from DNA sequences: A peculiar statistical estimation problem
    • (1995) Syst. Biol. , vol.44 , pp. 384-399
  • 70
    • 0033015735 scopus 로고    scopus 로고
    • Performance of likelihood ratio tests of evolutionary hypotheses under inadequate substitution models
    • (1999) Mol. Biol. Evol. , vol.16 , pp. 868-875
    • Zhang, J.1
  • 71
    • 0028108336 scopus 로고
    • Estimation of evolutionary distances between nucleotide sequences
    • (1994) J. Mol. Evol. , vol.39 , pp. 315-329
    • Zharkikh, A.1
  • 72
    • 0001895697 scopus 로고
    • Evolutionary divergence and convergence in proteins
    • V. Bryson and H. J. Vogel, eds. Evolving genes and proteins. Academic Press, N.Y.
    • (1965) , pp. 97-166
    • Zuckerkandl, E.1    Pauling, L.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.