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Volumn 15, Issue 7, 1998, Pages 910-917

Evolutionary distances for protein-coding sequences: Modeling site- specific residue frequencies

Author keywords

Evolutionary distances; Maximum likelihood; Saturation; Selection; Site specific frequencies; Variable rate models

Indexed keywords

AMINO ACID SEQUENCE; ARTICLE; EVOLUTION; GENE SEQUENCE; MATHEMATICAL ANALYSIS; MODEL;

EID: 0031875569     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/oxfordjournals.molbev.a025995     Document Type: Article
Times cited : (246)

References (36)
  • 3
    • 0029856518 scopus 로고    scopus 로고
    • Modeling residue usage in aligned protein sequences via maximum likelihood
    • _. 1996. Modeling residue usage in aligned protein sequences via maximum likelihood. Mol. Biol. Evol. 13: 1368-1375.
    • (1996) Mol. Biol. Evol. , vol.13 , pp. 1368-1375
  • 4
    • 0031453046 scopus 로고    scopus 로고
    • Estimation of reversible substitution matrices and evolutionary distance
    • BRUNO, W. J., and L. ARVESTAD. 1997. Estimation of reversible substitution matrices and evolutionary distance. J. Mol. Evol. 45:696-703.
    • (1997) J. Mol. Evol. , vol.45 , pp. 696-703
    • Bruno, W.J.1    Arvestad, L.2
  • 5
    • 0028926716 scopus 로고
    • Analysis of genomic sequences of 95 papillomavirus types - Uniting typing, phylogeny, and taxonomy
    • CHAN, S.-Y., H. DELIUIS, A. L. HALPERN, and H.-U. BERNARD. 1995. Analysis of genomic sequences of 95 papillomavirus types - uniting typing, phylogeny, and taxonomy. J. Virol. 69:3074-3083.
    • (1995) J. Virol. , vol.69 , pp. 3074-3083
    • Chan, S.-Y.1    Deliuis, H.2    Halpern, A.L.3    Bernard, H.-U.4
  • 7
    • 0029259085 scopus 로고
    • Maximum discrimination hidden Markov models of sequence consensus
    • EDDY, S. R., G. MITCHISON, and R. DURBIN. 1995. Maximum discrimination hidden Markov models of sequence consensus. J. Comput. Biol. 2:9-23.
    • (1995) J. Comput. Biol. , vol.2 , pp. 9-23
    • Eddy, S.R.1    Mitchison, G.2    Durbin, R.3
  • 8
    • 0025684868 scopus 로고
    • How old is the immunodeficiency virus?
    • EIGEN, M., and K. NIESELT-STRUWE. 1990. How old is the immunodeficiency virus? AIDS 4:S85-S93.
    • (1990) AIDS , vol.4
    • Eigen, M.1    Nieselt-Struwe, K.2
  • 9
    • 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
  • 10
    • 0003437299 scopus 로고
    • Distributed by author. Department of Genetics, University of Washington, Seattle
    • _. 1993. PHYLIP (phylogeny inference package). Version 3.5c. Distributed by author. Department of Genetics, University of Washington, Seattle.
    • (1993) PHYLIP (Phylogeny Inference Package). Version 3.5c
  • 11
    • 0030034795 scopus 로고    scopus 로고
    • A hidden Markov model approach to variation among sites in rate of evolution
    • FELSENSTEIN, J., and G. A. CHURCHILL. 1996. A hidden Markov model approach to variation among sites in rate of evolution. Mol. Biol. Evol. 13:93-104.
    • (1996) Mol. Biol. Evol. , vol.13 , pp. 93-104
    • Felsenstein, J.1    Churchill, G.A.2
  • 12
    • 0021070935 scopus 로고
    • Codon substitution in evolution and the "saturation" of synonymous changes
    • GOJOBORI, T. 1983. Codon substitution in evolution and the "saturation" of synonymous changes. Genetics 105:1011-1027.
    • (1983) Genetics , vol.105 , pp. 1011-1027
    • Gojobori, T.1
  • 13
    • 0020383449 scopus 로고
    • Estimation of average number of nucleotide substitutions when the rate of substitution varies with nucleotide
    • GOJOBORI, T., K. ISHII, and M. NEI. 1982. Estimation of average number of nucleotide substitutions when the rate of substitution varies with nucleotide. J. Mol. Evol. 18:414-423.
    • (1982) J. Mol. Evol. , vol.18 , pp. 414-423
    • Gojobori, T.1    Ishii, K.2    Nei, M.3
  • 14
    • 0025675724 scopus 로고
    • A maximum likelihood approach to the detection of selection from a phylogeny
    • GOLDING, B., and J. FELSENSTEIN. 1990. A maximum likelihood approach to the detection of selection from a phylogeny. J. Mol. Evol. 31:511-523.
    • (1990) J. Mol. Evol. , vol.31 , pp. 511-523
    • Golding, B.1    Felsenstein, J.2
  • 15
    • 0028168856 scopus 로고
    • A codon-based model of nucleotide substitution for protein-coding DNA sequences
    • GOLDMAN, N., and Z. YANG. 1994. A codon-based model of nucleotide substitution for protein-coding DNA sequences. Mol. Biol. Evol. 11:725-736.
    • (1994) Mol. Biol. Evol. , vol.11 , pp. 725-736
    • Goldman, N.1    Yang, Z.2
  • 16
    • 0029665409 scopus 로고    scopus 로고
    • Identification of sequence pattern with profile analysis
    • GRIBSKOV, M., and S. VERETNIK. 1996. Identification of sequence pattern with profile analysis. Methods Enzymol. 266:198-212.
    • (1996) Methods Enzymol. , vol.266 , pp. 198-212
    • Gribskov, M.1    Veretnik, S.2
  • 17
    • 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. 21:160-174.
    • (1985) J. Mol. Evol. , vol.21 , pp. 160-174
    • Hasegawa, M.1    Kishino, H.2    Yano, T.3
  • 18
    • 0029977162 scopus 로고    scopus 로고
    • Using substitution probabilities to improve position-specific scoring matrices
    • HENIKOFF, J. G., and S. HENIKOFF. 1996. Using substitution probabilities to improve position-specific scoring matrices. CABIOS 12:135-143.
    • (1996) CABIOS , vol.12 , pp. 135-143
    • Henikoff, J.G.1    Henikoff, S.2
  • 19
    • 0026458378 scopus 로고
    • Amino acid substitution matrices from protein blocks
    • HENIKOFF, S., and J. G. HENIKOFF. 1992. Amino acid substitution matrices from protein blocks. Proc. Natl. Acad. Sci. USA 3:10915-10919.
    • (1992) Proc. Natl. Acad. Sci. USA , vol.3 , pp. 10915-10919
    • Henikoff, S.1    Henikoff, J.G.2
  • 20
    • 0028118434 scopus 로고
    • Protein family classification based on searching a database of blocks
    • _. 1994. Protein family classification based on searching a database of blocks. Genomics 19:97-107.
    • (1994) Genomics , vol.19 , pp. 97-107
  • 21
    • 0004121963 scopus 로고
    • Regularizes for estimating distributions of amino acids from small samples
    • Technical report, University of California, Santa Cruz
    • KARPLUS, K. 1995a. Regularizes for estimating distributions of amino acids from small samples. Technical report, University of California, Santa Cruz. Technical Report UCSC-CRL-95-11, URL ftp://ftp.cse.ucsc.edu/pub/tr/ucsc-cr1-95-11.ps.Z.
    • (1995) Technical Report UCSC-CRL-95-11
    • Karplus, K.1
  • 22
    • 2642714019 scopus 로고
    • Regularizes for estimating distributions of amino acids from small samples
    • C. RAWLINGS, D. CLARK, R. ALTMAN, L. HUNTER, T. LENGAUER, and S. WODAK, eds. AAAI Press, Menlo Park, Calif.
    • _. 1995b. Regularizes for estimating distributions of amino acids from small samples. Pp. 188-196 in C. RAWLINGS, D. CLARK, R. ALTMAN, L. HUNTER, T. LENGAUER, and S. WODAK, eds. ISMB-95: Proceedings, Third International Conference on Intelligent Systems for Molecular Biology. AAAI Press, Menlo Park, Calif.
    • (1995) ISMB-95: Proceedings, Third International Conference on Intelligent Systems for Molecular Biology , pp. 188-196
  • 23
    • 0000800333 scopus 로고
    • On the probability of fixation of mutant genes in a population
    • KIMURA, M. 1962. On the probability of fixation of mutant genes in a population. Genetics 4:713-719.
    • (1962) Genetics , vol.4 , pp. 713-719
    • Kimura, M.1
  • 24
    • 0028181441 scopus 로고
    • Hidden Markov models in computational biology: Applications to protein modeling
    • KROGH, A., M. BROWN, I. S. MIAN, K. SJOLANDER, and D. HAUSSLER. 1994. Hidden Markov models in computational biology: applications to protein modeling. J. Mol. Biol. 235: 1501-1531.
    • (1994) J. Mol. Biol. , vol.235 , pp. 1501-1531
    • Krogh, A.1    Brown, M.2    Mian, I.S.3    Sjolander, K.4    Haussler, D.5
  • 25
    • 0031892789 scopus 로고    scopus 로고
    • A genetic algorithm for maximum-likelihood phylogeny inference using nucleotide sequence data
    • LEWIS, P. O. 1998. A genetic algorithm for maximum-likelihood phylogeny inference using nucleotide sequence data. Mol. Biol. Evol. 15:277-283.
    • (1998) Mol. Biol. Evol. , vol.15 , pp. 277-283
    • Lewis, P.O.1
  • 26
    • 0029565880 scopus 로고
    • Tree-based maximal likelihood substitution matrices and hidden Markov models
    • MITCHISON, G., and R. DURBIN. 1995. Tree-based maximal likelihood substitution matrices and hidden Markov models. J. Mol. Evol. 41:1139-1151.
    • (1995) J. Mol. Evol. , vol.41 , pp. 1139-1151
    • Mitchison, G.1    Durbin, R.2
  • 27
    • 0028024626 scopus 로고
    • A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome
    • MUSE, S. V., and B. S. GAUT. 1994. A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome. Mol. Biol. Evol. 11:715-724.
    • (1994) Mol. Biol. Evol. , vol.11 , pp. 715-724
    • Muse, S.V.1    Gaut, B.S.2
  • 28
    • 0003518435 scopus 로고    scopus 로고
    • Human papillomaviruses 1996, a compilation and analysis of nucleic acid and amino acid sequences
    • Los Alamos National Laboratory, Los Alamos, N.M.
    • MYERS, G., A. HALPERN, C. BAKER, A. MCBRIDE, C. WHEELER, and J. DOORBAR. 1996. Human papillomaviruses 1996, a compilation and analysis of nucleic acid and amino acid sequences. Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, N.M.
    • (1996) Theoretical Biology and Biophysics
    • Myers, G.1    Halpern, A.2    Baker, C.3    Mcbride, A.4    Wheeler, C.5    Doorbar, J.6
  • 29
    • 0026606297 scopus 로고
    • The emergence of simian/human immunodeficiency viruses
    • MYERS, G., K. MACINNES, and B. KORBER. 1992. The emergence of simian/human immunodeficiency viruses. AIDS Res. Hum. Retroviruses 8:373-386.
    • (1992) AIDS Res. Hum. Retroviruses , vol.8 , pp. 373-386
    • Myers, G.1    Macinnes, K.2    Korber, B.3
  • 30
    • 0027957393 scopus 로고
    • fastDNAm1 - A tool for construction of phylogenetic trees of DNA sequences using maximum likelihood
    • OLSEN, G. J., H. MATSUDA, R. HAGSTROM, and R. OVERBEEK. 1994. fastDNAm1 - a tool for construction of phylogenetic trees of DNA sequences using maximum likelihood. CABIOS 10:41-48.
    • (1994) CABIOS , vol.10 , pp. 41-48
    • Olsen, G.J.1    Matsuda, H.2    Hagstrom, R.3    Overbeek, R.4
  • 31
    • 0029906607 scopus 로고    scopus 로고
    • Dirichlet mixtures: A method for improving detection of weak but significant protein sequence homology
    • SOJLANDER, K., K. KARPLUS, M. BROWN, R. HUGHEY, A. KROGH, I. S. MIAN, and D. HAUSSLER. 1996. Dirichlet mixtures: a method for improving detection of weak but significant protein sequence homology. CABIOS 12:327-345.
    • (1996) CABIOS , vol.12 , pp. 327-345
    • Sojlander, K.1    Karplus, K.2    Brown, M.3    Hughey, R.4    Krogh, A.5    Mian, I.S.6    Haussler, D.7
  • 32
    • 0001336205 scopus 로고    scopus 로고
    • Phylogenetic inference
    • D. M. HILLIS, C. MORITZ, and B. K. MABLE, eds. Sinauer, Sunderland, Mass.
    • SWOFFORD, D. L., G. J. OLSEN, P. J. WADDELL, and D. M. HILLIS. 1996. Phylogenetic inference. Pp. 407-514 in D. M. HILLIS, C. MORITZ, and B. K. MABLE, eds. Molecular Systematics. 2nd edition. Sinauer, Sunderland, Mass.
    • (1996) Molecular Systematics. 2nd Edition , pp. 407-514
    • Swofford, D.L.1    Olsen, G.J.2    Waddell, P.J.3    Hillis, D.M.4
  • 33
    • 0029985399 scopus 로고    scopus 로고
    • Combining protein evolution and secondary structure
    • THORNE, J. L., N. GOLDMAN, and D. T. JONES. 1996. Combining protein evolution and secondary structure. Mol. Biol. Evol. 13:666-673.
    • (1996) Mol. Biol. Evol. , vol.13 , pp. 666-673
    • Thorne, J.L.1    Goldman, N.2    Jones, D.T.3
  • 34
    • 0030425648 scopus 로고    scopus 로고
    • Molecular evidence for deep pre-Cambrian divergences among metazoan phyla
    • WRAY, G. A., J. S. LEVINTON, and L. H. SHAPIRO. 1996. Molecular evidence for deep pre-Cambrian divergences among metazoan phyla. Science 274:568-573.
    • (1996) Science , vol.274 , pp. 568-573
    • Wray, G.A.1    Levinton, J.S.2    Shapiro, L.H.3
  • 36
    • 0030451420 scopus 로고    scopus 로고
    • Among-site rate variation and its impact on phylogenetic distances
    • _. 1996. Among-site rate variation and its impact on phylogenetic distances. Trends Ecol. Evol. 11:367-372.
    • (1996) Trends Ecol. Evol. , vol.11 , pp. 367-372


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