메뉴 건너뛰기




Volumn 14, Issue 11, 1997, Pages 1106-1113

A simple method for estimating the parameter of substitution rate variation among sites

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SUBSTITUTION; ARTICLE; GENE REARRANGEMENT; GENETIC VARIABILITY; MATHEMATICAL ANALYSIS;

EID: 0030734575     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/oxfordjournals.molbev.a025720     Document Type: Article
Times cited : (117)

References (36)
  • 2
    • 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
  • 3
    • 84959747425 scopus 로고
    • Toward defining the course of evolution: Minimum change for a specific tree topology
    • FITCH, W. M. 1971. Toward defining the course of evolution: minimum change for a specific tree topology. Syst. Zool. 20:406-416.
    • (1971) Syst. Zool. , vol.20 , pp. 406-416
    • Fitch, W.M.1
  • 4
    • 0030857505 scopus 로고    scopus 로고
    • The age of common ancestor of eukaryotes and prokaryotes: Statistical inferences
    • GU, X. 1997. The age of common ancestor of eukaryotes and prokaryotes: statistical inferences. Mol. Biol. Evol. 14:861-866.
    • (1997) Mol. Biol. Evol. , vol.14 , pp. 861-866
    • Gu, X.1
  • 5
    • 0029068893 scopus 로고
    • Maximum likelihood estimation of the heterogeneity of substitution rate among nucleotide sites
    • GU, X., Y. X. FU, and W. H. LI. 1995. Maximum likelihood estimation of the heterogeneity of substitution rate among nucleotide sites. Mol. Biol. Evol. 12:546-557.
    • (1995) Mol. Biol. Evol. , vol.12 , pp. 546-557
    • Gu, X.1    Fu, Y.X.2    Li, W.H.3
  • 6
    • 0029900516 scopus 로고    scopus 로고
    • A general additive distance with time-reversibility and rale variation among nucleotide sites
    • Gu, X., and W. H. LI. 1996. A general additive distance with time-reversibility and rale variation among nucleotide sites. Proc. Natl. Acad. Sci. USA 93:4671-4676.
    • (1996) Proc. Natl. Acad. Sci. USA , vol.93 , pp. 4671-4676
    • Gu, X.1    Li, W.H.2
  • 7
    • 0021017159 scopus 로고
    • The spatial distribution of fixed mutations within genes coding for proteins
    • HOLMQUIST, R., M. GOODMAN, T. CONROY, and J. CZELUSNIAK. 1983. The spatial distribution of fixed mutations within genes coding for proteins. J. Mol. Evol. 19:437-448.
    • (1983) J. Mol. Evol. , vol.19 , pp. 437-448
    • Holmquist, R.1    Goodman, M.2    Conroy, T.3    Czelusniak, J.4
  • 8
    • 12044255023 scopus 로고
    • Success of phylogenetic methods in the four-taxon case
    • HUELSENBECK, J., and D. M. HILLIS. 1993. Success of phylogenetic methods in the four-taxon case. Syst. Biol. 42:247-264.
    • (1993) Syst. Biol. , vol.42 , pp. 247-264
    • Huelsenbeck, J.1    Hillis, D.M.2
  • 9
    • 0025061094 scopus 로고
    • Limitations of the evolutionary parsimony method of phylogenetic analysis
    • JIN, L., und M. NEI. 1990. Limitations of the evolutionary parsimony method of phylogenetic analysis. Mol. Biol. Evol. 7:82-102.
    • (1990) Mol. Biol. Evol. , vol.7 , pp. 82-102
    • Jin, L.1    Nei, M.2
  • 11
    • 0026691182 scopus 로고
    • The rapid generation of mutation data matrices from protein sequences
    • JONES, D. T., W. R. TAYLOR, and J. M. THORNTON. 1992. The rapid generation of mutation data matrices From protein sequences. Comput. Appl. Biosci. 8:275-282.
    • (1992) Comput. Appl. Biosci. , vol.8 , pp. 275-282
    • Jones, D.T.1    Taylor, W.R.2    Thornton, J.M.3
  • 12
    • 0000732090 scopus 로고
    • Evolution of protein molecules
    • H. R. MUNRO, ed. Academic Press, New York
    • JUKES, T. H., and C. R. CANTOR. 1969. Evolution of protein molecules. Pp. 21-32 in H. R. MUNRO, ed. Mammalian protein metabolism. Vol. 3. Academic Press, New York.
    • (1969) Mammalian Protein Metabolism , vol.3 , pp. 21-32
    • Jukes, T.H.1    Cantor, C.R.2
  • 13
    • 0029930086 scopus 로고    scopus 로고
    • Modeling nucleotide evolution: A heterogeneous rate analysis
    • KELLY, C., and J. RICE. 1996. Modeling nucleotide evolution: a heterogeneous rate analysis. Math. Biosci. 133:85-109.
    • (1996) Math. Biosci. , vol.133 , pp. 85-109
    • Kelly, C.1    Rice, J.2
  • 14
    • 0019296687 scopus 로고
    • A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences
    • KIMURA, M. 1980. A simple method for estimating evolutionary rate 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
  • 15
    • 0029881442 scopus 로고    scopus 로고
    • Probabilistic reconstruction of ancestral protein sequences
    • KOSHI, M., and R. A. GOLDSTEIN. 1996. Probabilistic reconstruction of ancestral protein sequences. J. Mol. Evol. 42:313-320.
    • (1996) J. Mol. Evol. , vol.42 , pp. 313-320
    • Koshi, M.1    Goldstein, R.A.2
  • 16
    • 0000129603 scopus 로고
    • Evolutionary analysis of length-variable sequences: Divergent domains of ribosomal RNA
    • M. M. MIYAMOTO and J. CRACRAFT, eds. Oxford University Press, Oxford
    • LARSON, A. 1991. Evolutionary analysis of length-variable sequences: divergent domains of ribosomal RNA. Pp. 221-248 in M. M. MIYAMOTO and J. CRACRAFT, eds. Phylogenetic analysis of DNA sequences. Oxford University Press, Oxford.
    • (1991) Phylogenetic Analysis of DNA Sequences , pp. 221-248
    • Larson, A.1
  • 17
    • 0028229606 scopus 로고
    • Reconstruction of ancestral sequences by the inferred method, a tool for protein engineering studies
    • LIBERTINI, G., and A. DI DONATO. 1994. Reconstruction of ancestral sequences by the inferred method, a tool for protein engineering studies. J. Mol. Evol. 39:219-229.
    • (1994) J. Mol. Evol. , vol.39 , pp. 219-229
    • Libertini, G.1    Di Donato, A.2
  • 18
    • 0030309433 scopus 로고    scopus 로고
    • Constraints on protein evolution and the age of the eubacteria/eukaryote split
    • MIYAMOTO, M. M., and W. M. FITCH. 1996. Constraints on protein evolution and the age of the eubacteria/eukaryote split. Syst. Biol. 45:568-575.
    • (1996) Syst. Biol. , vol.45 , pp. 568-575
    • Miyamoto, M.M.1    Fitch, W.M.2
  • 19
    • 0030458552 scopus 로고    scopus 로고
    • Phylogenetic analysis in molecular evolutionary genetics
    • NEI, M. 1996. Phylogenetic analysis in molecular evolutionary genetics. Annu. Rev. Genet. 30:371-403.
    • (1996) Annu. Rev. Genet. , vol.30 , pp. 371-403
    • Nei, M.1
  • 20
    • 0031153858 scopus 로고    scopus 로고
    • Site-by-site estimation of the rate of substitution and me correlation of rates in mitochondrial DNA
    • NIELSEN, R. 1997. Site-by-site estimation of the rate of substitution and me correlation of rates in mitochondrial DNA. Syst. Biol. 46:346-357.
    • (1997) Syst. Biol. , vol.46 , pp. 346-357
    • Nielsen, R.1
  • 21
    • 0028338820 scopus 로고
    • Estimation of the number of amino acid substitutions per site when the substitution rate varies among sites
    • OTA, T., and M. NEI. 1994. Estimation of the number of amino acid substitutions per site when the substitution rate varies among sites. J. Mol. Evol. 38:642-643.
    • (1994) J. Mol. Evol. , vol.38 , pp. 642-643
    • Ota, T.1    Nei, M.2
  • 22
    • 0030045281 scopus 로고    scopus 로고
    • Efficiencies of different genes and different tree-building methods in recovering a known vertebrate phylogeny
    • RUSSO, A. M., N. TAKEZAKI, and M. NEI. 1996. Efficiencies of different genes and different tree-building methods in recovering a known vertebrate phylogeny. Mol. Biol. Evol. 13:525-536.
    • (1996) Mol. Biol. Evol. , vol.13 , pp. 525-536
    • Russo, A.M.1    Takezaki, N.2    Nei, M.3
  • 23
    • 0029149610 scopus 로고
    • Uncertainty in ancient phylogenies
    • SCHLUTER, D. 1995. Uncertainty in ancient phylogenies. Nature 377:108-109.
    • (1995) Nature , vol.377 , pp. 108-109
    • Schluter, D.1
  • 24
    • 0028807391 scopus 로고
    • Amongsite rate variation and phylogenetic analysis of 12S rRNA in Sigmontine rodents
    • SULLIVAN, J., K. E. HOLSINGER, and C. SIMON. 1995. Amongsite rate variation and phylogenetic analysis of 12S rRNA in Sigmontine rodents. Mol. Biol. Evol. 12:988-1001.
    • (1995) Mol. Biol. Evol. , vol.12 , pp. 988-1001
    • Sullivan, J.1    Holsinger, K.E.2    Simon, C.3
  • 25
    • 0021716351 scopus 로고
    • Estimation of evolutionary distances between nucleotide sequences
    • TAJIMA, F., and M. NEI. 1984. Estimation of evolutionary distances between nucleotide sequences. Mol. Biol. Evol. 1:269-285.
    • (1984) Mol. Biol. Evol. , vol.1 , pp. 269-285
    • Tajima, F.1    Nei, M.2
  • 26
    • 0027157960 scopus 로고
    • Estimating of the number of nucleotide substitutions in the control region of mitocondrial DNA in humans and chimpanzees
    • TAMURA, K., and M. NEI. 1993. Estimating of the number of nucleotide substitutions in the control region of mitocondrial DNA in humans and chimpanzees. Mol. Biol. Evol. 10:512-526.
    • (1993) Mol. Biol. Evol. , vol.10 , pp. 512-526
    • Tamura, K.1    Nei, M.2
  • 27
    • 0028205953 scopus 로고
    • Relative efficiencies of the maximum-likelihood, neighbor-jointing, and maximum-parsimory methods when substitution rate varies with sites
    • TATENO, Y., N. TAKEZAKI, and M. NEI. 1994. Relative efficiencies of the maximum-likelihood, neighbor-jointing, and maximum-parsimory methods when substitution rate varies with sites. Mol. Biol. Evol. 11:261-277.
    • (1994) Mol. Biol. Evol. , vol.11 , pp. 261-277
    • Tateno, Y.1    Takezaki, N.2    Nei, M.3
  • 28
    • 0031046929 scopus 로고    scopus 로고
    • Evolutionary distances between nucleotide sequences based on the distribution of substitution rates among sites as estimated by parsimony
    • TOURASSE, N., and M. GOUY. 1997. Evolutionary distances between nucleotide sequences based on the distribution of substitution rates among sites as estimated by parsimony. Mol. Biol. Evol. 14:287-298.
    • (1997) Mol. Biol. Evol. , vol.14 , pp. 287-298
    • Tourasse, N.1    Gouy, M.2
  • 29
    • 0015219691 scopus 로고
    • Filling discrete probability distributions to evolutionary events
    • UZZEL, T., and K. W. CORBIN. 1971. Filling discrete probability distributions to evolutionary events. Science 172:1089-1096.
    • (1971) Science , vol.172 , pp. 1089-1096
    • Uzzel, T.1    Corbin, K.W.2
  • 30
    • 0027496790 scopus 로고
    • Substitution rate variation among sites in hypervariable region I of human mitochondrial DNA
    • WAKELEY, J. 1993. Substitution rate variation among sites in hypervariable region I of human mitochondrial DNA. J. Mol. Evol. 37:613-623.
    • (1993) J. Mol. Evol. , vol.37 , pp. 613-623
    • Wakeley, J.1
  • 31
    • 0027132974 scopus 로고
    • Maximum-likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites
    • YANG, Z. 1993. Maximum-likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites. Mol. Biol. Evol. 10:1396-1401.
    • (1993) Mol. Biol. Evol. , vol.10 , pp. 1396-1401
    • Yang, Z.1
  • 32
    • 0028064845 scopus 로고
    • Maximum likelihood estimation of phylogeny from DNA sequences when substitute rates differ over sites: Approximate methods
    • _. 1994. Maximum likelihood estimation of phylogeny from DNA sequences when substitute rates differ over sites: approximate methods. J. Mol. Evol. 39:306-314.
    • (1994) J. Mol. Evol. , vol.39 , pp. 306-314
  • 33
    • 0030451420 scopus 로고    scopus 로고
    • Among-site rate variation and ils impact on phylogenetic analysis
    • _. 1996. Among-site rate variation and ils impact on phylogenetic analysis. Trends Ecol. Evol. 11:367-372.
    • (1996) Trends Ecol. Evol. , vol.11 , pp. 367-372
  • 34
    • 0029892459 scopus 로고    scopus 로고
    • Approximate methods for estimating the pattern of nucleotide substitution and the variation of substitution rates among sites
    • YANG, Z., and S. KUMAR. 1996. Approximate methods for estimating the pattern of nucleotide substitution and the variation of substitution rates among sites. Mol. Biol. Evol. 13:650-659.
    • (1996) Mol. Biol. Evol. , vol.13 , pp. 650-659
    • Yang, Z.1    Kumar, S.2
  • 35
    • 0028820333 scopus 로고
    • A new method of inference of ancestral nudeotide and amino acid sequences
    • YANG, Z., S. KUMAR, and M. NEI. 1995. A new method of inference of ancestral nudeotide and amino acid sequences. Genetics 141:1641-1650.
    • (1995) Genetics , vol.141 , pp. 1641-1650
    • Yang, Z.1    Kumar, S.2    Nei, M.3
  • 36
    • 0031025677 scopus 로고    scopus 로고
    • Accuracies of ancestral amino acid sequences interred by the parsimony, likelihood, and distance methods
    • ZHANG, J., and M. NEI. 1997. Accuracies of ancestral amino acid sequences interred by the parsimony, likelihood, and distance methods. J. Mol. Evol. 44(Suppl. 1):S139-S146.
    • (1997) J. Mol. Evol. , vol.44 , Issue.SUPPL. 1
    • Zhang, J.1    Nei, M.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.