메뉴 건너뛰기




Volumn 22, Issue 12, 2005, Pages 2472-2479

Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level

Author keywords

Branch site model; Computer simulation; Likelihood ratio test; Positive selection

Indexed keywords

ANALYTIC METHOD; ARTICLE; COMPUTER SIMULATION; DNA SEQUENCE; EVALUATION; GENE CONSTRUCT; GENETIC SELECTION; MOLECULAR GENETICS; NUCLEOTIDE BINDING SITE; RELIABILITY; SEQUENCE ANALYSIS; SIGNAL TRANSDUCTION; THEORETICAL MODEL;

EID: 27844439855     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msi237     Document Type: Article
Times cited : (1416)

References (20)
  • 1
    • 0033999304 scopus 로고    scopus 로고
    • The phytochrome gene family in tomato and the rapid differential evolution of this family in angiosperms
    • Alba, R., P. M. Kelmenson, M.-M. Cordonnier-Pratt, and L. H. Pratt. 2000. The phytochrome gene family in tomato and the rapid differential evolution of this family in angiosperms. Mol. Biol. Evol. 17:362-373.
    • (2000) Mol. Biol. Evol. , vol.17 , pp. 362-373
    • Alba, R.1    Kelmenson, P.M.2    Cordonnier-Pratt, M.-M.3    Pratt, L.H.4
  • 2
    • 0000926206 scopus 로고
    • On the distribution of the likelihood ratio
    • Chernoff, H. 1954. On the distribution of the likelihood ratio. Ann. Math. Stat. 25:573-578.
    • (1954) Ann. Math. Stat. , vol.25 , pp. 573-578
    • Chernoff, H.1
  • 4
    • 0031033277 scopus 로고    scopus 로고
    • Episodic adaptive evolution of primate lysozymes
    • Messier, W. and C.-B. Stewart. 1997. Episodic adaptive evolution of primate lysozymes. Nature 385:151-154.
    • (1997) Nature , vol.385 , pp. 151-154
    • Messier, W.1    Stewart, C.-B.2
  • 6
    • 0031972161 scopus 로고    scopus 로고
    • Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene
    • Nielsen, R. and Z. Yang. 1998. Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene. Genetics 148:929-936.
    • (1998) Genetics , vol.148 , pp. 929-936
    • Nielsen, R.1    Yang, Z.2
  • 7
    • 84907319426 scopus 로고
    • Asymptotic properties of maximum likelihood estimators and likelihood ratio tests under nonstandard conditions
    • Self, S. G. and K.-Y. Liang. 1987. Asymptotic properties of maximum likelihood estimators and likelihood ratio tests under nonstandard conditions. J. Am. Stat. Assoc. 82:605-610.
    • (1987) J. Am. Stat. Assoc. , vol.82 , pp. 605-610
    • Self, S.G.1    Liang, K.-Y.2
  • 8
    • 0023666025 scopus 로고
    • Adaptive evolution in the stomach lysozymes of foregut fermenters
    • Stewart, C.-B., J. W. Schilling, and A. C. Wilson. 1987. Adaptive evolution in the stomach lysozymes of foregut fermenters. Nature 330:401-404.
    • (1987) Nature , vol.330 , pp. 401-404
    • Stewart, C.-B.1    Schilling, J.W.2    Wilson, A.C.3
  • 9
    • 0032849322 scopus 로고    scopus 로고
    • A method for detecting positive selection at single amino acid sites
    • Suzuki, Y. and T. Gojobori. 1999. A method for detecting positive selection at single amino acid sites. Mol. Biol. Evol. 16:1315-1328.
    • (1999) Mol. Biol. Evol. , vol.16 , pp. 1315-1328
    • Suzuki, Y.1    Gojobori, T.2
  • 10
    • 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
  • 11
    • 0031897964 scopus 로고    scopus 로고
    • Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution
    • Yang, Z. 1998. Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution. Mol. Biol. Evol. 15:568-573.
    • (1998) Mol. Biol. Evol. , vol.15 , pp. 568-573
    • Yang, Z.1
  • 12
    • 0036889183 scopus 로고    scopus 로고
    • Inference of selection from multiple species alignments
    • Yang, Z. 2002. Inference of selection from multiple species alignments. Curr. Opin. Genet. Dev. 12:688-694.
    • (2002) Curr. Opin. Genet. Dev. , vol.12 , pp. 688-694
    • Yang, Z.1
  • 13
    • 0033639150 scopus 로고    scopus 로고
    • Statistical methods for detecting molecular adaptation
    • Yang, Z. and J. P. Bielawski. 2000. Statistical methods for detecting molecular adaptation. Trends Ecol. Evol. 15:496-503.
    • (2000) Trends Ecol. Evol. , vol.15 , pp. 496-503
    • Yang, Z.1    Bielawski, J.P.2
  • 14
    • 0036270185 scopus 로고    scopus 로고
    • Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages
    • Yang, Z. and R. Nielsen. 2002. Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages. Mol. Biol. Evol. 19:908-917.
    • (2002) Mol. Biol. Evol. , vol.19 , pp. 908-917
    • Yang, Z.1    Nielsen, R.2
  • 15
    • 0034097381 scopus 로고    scopus 로고
    • Codon-substitution models for heterogeneous selection pressure at amino acid sites
    • Yang, Z., R. Nielsen, N. Goldman, and A.-M. K. Pedersen. 2000. Codon-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.K.4
  • 16
    • 16344378246 scopus 로고    scopus 로고
    • Bayes empirical Bayes inference of amino acid sites under positive selection
    • Yang, Z., W. S. W. Wong, and R. Nielsen. 2005. Bayes empirical Bayes inference of amino acid sites under positive selection. Mol. Biol. Evol. 22:1107-1118.
    • (2005) Mol. Biol. Evol. , vol.22 , pp. 1107-1118
    • Yang, Z.1    Wong, W.S.W.2    Nielsen, R.3
  • 17
    • 0030124771 scopus 로고    scopus 로고
    • Evolution of stomach lysozyme: The pig lysozyme gene
    • Yu, M. and D. M. Irwin. 1996. Evolution of stomach lysozyme: the pig lysozyme gene. Mol. Phylogenet. Evol. 5: 298-308.
    • (1996) Mol. Phylogenet. Evol. , vol.5 , pp. 298-308
    • Yu, M.1    Irwin, D.M.2
  • 18
    • 3042637218 scopus 로고    scopus 로고
    • Frequent false detection of positive selection by the likelihood method with branch-site models
    • Zhang, J. 2004. Frequent false detection of positive selection by the likelihood method with branch-site models. Mol. Biol. Evol. 21:1332-1339.
    • (2004) Mol. Biol. Evol. , vol.21 , pp. 1332-1339
    • Zhang, J.1
  • 19
    • 0031306932 scopus 로고    scopus 로고
    • Small-sample tests of episodic adaptive evolution: A case study of primate lysozymes
    • Zhang, J., S. Kumar, and M. Nei. 1997. Small-sample tests of episodic adaptive evolution: a case study of primate lysozymes. Mol. Biol. Evol. 14:1335-1338.
    • (1997) Mol. Biol. Evol. , vol.14 , pp. 1335-1338
    • Zhang, J.1    Kumar, S.2    Nei, M.3
  • 20
    • 0032584099 scopus 로고    scopus 로고
    • Positive Darwinian selection after gene duplication in primate ribonuclease genes
    • USA
    • Zhang, J., H. F. Rosenberg, and M. Nei. 1998. Positive Darwinian selection after gene duplication in primate ribonuclease genes. Proc. Natl. Acad. Sci. USA 95:3708-3713.
    • (1998) Proc. Natl. Acad. Sci. , vol.95 , pp. 3708-3713
    • Zhang, J.1    Rosenberg, H.F.2    Nei, M.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.