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Volumn 16, Issue 2, 2000, Pages 130-134

TOPAL 2.0: Improved detection of mosaic sequences within multiple alignments

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; MATHEMATICAL MODEL; PHYLOGENY; PRIORITY JOURNAL; STATISTICAL ANALYSIS;

EID: 0034097468     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/16.2.130     Document Type: Article
Times cited : (119)

References (23)
  • 1
    • 84959798530 scopus 로고
    • Cases in which parsimony or compatibility methods will be positively misleading
    • Felsenstein, J. (1978) Cases in which parsimony or compatibility methods will be positively misleading. Syst. Zool., 27, 401-410.
    • (1978) Syst. Zool. , vol.27 , pp. 401-410
    • Felsenstein, J.1
  • 2
    • 0031041347 scopus 로고    scopus 로고
    • A likelihood method for the detection of selection and recombination using nucleotide sequences
    • Grassly, N.C. and Holmes, E.C. (1997) A likelihood method for the detection of selection and recombination using nucleotide sequences. Mol. Biol. Evol., 14, 239-247.
    • (1997) Mol. Biol. Evol. , vol.14 , pp. 239-247
    • Grassly, N.C.1    Holmes, E.C.2
  • 3
    • 0030670413 scopus 로고    scopus 로고
    • Pseq-gen: An application for the Monte Carlo simulation of protein sequence evolution along phylogenetic trees
    • Grassly, N.C., Adachi, J. and Rambaut, A. (1997) Pseq-gen: an application for the Monte Carlo simulation of protein sequence evolution along phylogenetic trees. CABIOS, 13, 559-560.
    • (1997) CABIOS , vol.13 , pp. 559-560
    • Grassly, N.C.1    Adachi, J.2    Rambaut, A.3
  • 4
    • 0030498194 scopus 로고    scopus 로고
    • Ancestral inference from samples of DNA sequences with recombination
    • Griffiths, R.C. and Marjoram, P. (1996) Ancestral inference from samples of DNA sequences with recombination. J. Comput. Biol., 3, 479-502.
    • (1996) J. Comput. Biol. , vol.3 , pp. 479-502
    • Griffiths, R.C.1    Marjoram, P.2
  • 5
    • 0027471670 scopus 로고
    • A heuristic method to reconstruct the history of sequences subject to recombination
    • Hein, J. (1993) A heuristic method to reconstruct the history of sequences subject to recombination. J. Mol. Evol., 36, 396-405.
    • (1993) J. Mol. Evol. , vol.36 , pp. 396-405
    • Hein, J.1
  • 6
    • 0002410257 scopus 로고    scopus 로고
    • Parametric bootstrapping in molecular phylogenetics: Applications and performance
    • Ferraris, J.D. and Palumbi, S.R. (eds), Wiley-Liss, New York
    • Huelsenbeck, J.P., Hillis, D.M. and Jones, R. (1996) Parametric bootstrapping in molecular phylogenetics: applications and performance. In Ferraris, J.D. and Palumbi, S.R. (eds), Molecular Zoology: Advances, Strategies and Protocols Wiley-Liss, New York, pp. 19-45.
    • (1996) Molecular Zoology: Advances, Strategies and Protocols , pp. 19-45
    • Huelsenbeck, J.P.1    Hillis, D.M.2    Jones, R.3
  • 7
    • 0000732090 scopus 로고
    • Evolution of protein molecules
    • Munro, H.N. (ed.), Academic Press, New York
    • Jukes, T.H. and Cantor, C.R. (1969) Evolution of protein molecules. In Munro, H.N. (ed.), Mammalian Protein Metabolism Academic Press, New York, pp. 21-132.
    • (1969) Mammalian Protein Metabolism , pp. 21-132
    • Jukes, T.H.1    Cantor, C.R.2
  • 8
    • 0019296687 scopus 로고
    • A simple model for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences
    • Kimura, M. (1980) A simple model 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
  • 10
    • 85038040233 scopus 로고    scopus 로고
    • LAMARC
    • Kuhner, M.K. and Yamato, J. (1998) LAMARC. Available at http: //evolution.genetics.washington.edu/lamarc.html.
    • (1998)
    • Kuhner, M.K.1    Yamato, J.2
  • 11
    • 0026771340 scopus 로고
    • Inference of horizontal genetic transfer from molecular data: An approach using the bootstrap
    • Lawrence, J.G. and Hartl, D.L. (1992) Inference of horizontal genetic transfer from molecular data: an approach using the bootstrap. Genetics, 131, 753-760.
    • (1992) Genetics , vol.131 , pp. 753-760
    • Lawrence, J.G.1    Hartl, D.L.2
  • 12
    • 0026708873 scopus 로고
    • Analyzing the mosaic structure of genes
    • Maynard Smith, J. (1992) Analyzing the mosaic structure of genes. J. Mol. Evol., 34, 126-129.
    • (1992) J. Mol. Evol. , vol.34 , pp. 126-129
    • Maynard Smith, J.1
  • 13
    • 0031897789 scopus 로고    scopus 로고
    • Detecting recombination from gene trees
    • Maynard Smith, J. and Smith, N.H. (1998) Detecting recombination from gene trees. Mol. Biol. Evol., 15, 590-599.
    • (1998) Mol. Biol. Evol. , vol.15 , pp. 590-599
    • Maynard Smith, J.1    Smith, N.H.2
  • 14
    • 0031857686 scopus 로고    scopus 로고
    • TOPAL: Recombination detection in DNA and protein sequences
    • McGuire, G. and Wright, F. (1998) TOPAL: recombination detection in DNA and protein sequences. Bioinformatics, 14, 219-220.
    • (1998) Bioinformatics , vol.14 , pp. 219-220
    • McGuire, G.1    Wright, F.2
  • 15
    • 0030732297 scopus 로고    scopus 로고
    • A graphical method for detecting recombination in phylogenetic data sets
    • McGuire, G., Wright, F. and Prentice, M.J. (1997) A graphical method for detecting recombination in phylogenetic data sets. Mol. Biol. Evol., 14, 1125-1131.
    • (1997) Mol. Biol. Evol. , vol.14 , pp. 1125-1131
    • McGuire, G.1    Wright, F.2    Prentice, M.J.3
  • 16
    • 0032712498 scopus 로고    scopus 로고
    • Improved error bounds for genetic distances from DNA sequences
    • in press
    • McGuire, G., Prentice, M.J. and Wright, F. (1999) Improved error bounds for genetic distances from DNA sequences. Biometrics, in press.
    • (1999) Biometrics
    • McGuire, G.1    Prentice, M.J.2    Wright, F.3
  • 17
    • 0034048880 scopus 로고    scopus 로고
    • A Bayesian model for detecting past recombination events in DNA multiple alignments
    • in press
    • McGuire, G., Wright, F. and Prentice, M.J. (2000) A Bayesian model for detecting past recombination events in DNA multiple alignments. J. Comput. Biol., in press.
    • (2000) J. Comput. Biol.
    • McGuire, G.1    Wright, F.2    Prentice, M.J.3
  • 18
    • 0030928378 scopus 로고    scopus 로고
    • Seq-Gen: An application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees
    • Rambaut, A. and Grassly, N.C. (1997) Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. CABIOS, 13, 235-238.
    • (1997) CABIOS , vol.13 , pp. 235-238
    • Rambaut, A.1    Grassly, N.C.2
  • 19
    • 0023375195 scopus 로고
    • The neighbor-joining method: A new method for reconstructing phylognetic trees
    • Saitou, N. and Nei, M. (1987) The neighbor-joining method: a new method for reconstructing phylognetic trees. Mol. Biol. Evol., 4, 406-425.
    • (1987) Mol. Biol. Evol. , vol.4 , pp. 406-425
    • Saitou, N.1    Nei, M.2
  • 20
    • 0028793170 scopus 로고
    • Identification of breakpoints in intergenotypic recombinants of HIV type 1 by bootscanning
    • Salminen, M.O., Carr, J.K., Burke, D.S. and McCutchan, F.E. (1995) Identification of breakpoints in intergenotypic recombinants of HIV type 1 by bootscanning. AIDS Res. Hum. Retroviruses, 11, 1423-1425.
    • (1995) AIDS Res. Hum. Retroviruses , vol.11 , pp. 1423-1425
    • Salminen, M.O.1    Carr, J.K.2    Burke, D.S.3    McCutchan, F.E.4
  • 21
    • 0024356449 scopus 로고
    • Statistical tests for detecting gene conversion
    • Sawyer, S. (1989) Statistical tests for detecting gene conversion. Mol. Biol. Evol., 6, 526-538.
    • (1989) Mol. Biol. Evol. , vol.6 , pp. 526-538
    • Sawyer, S.1
  • 22
    • 0022410317 scopus 로고
    • Statistical methods of DNA sequence analysis: Detection of intragenic recombination or gene conversion
    • Stephens, J.C. (1985) Statistical methods of DNA sequence analysis: detection of intragenic recombination or gene conversion. Mol. Biol. Evol., 2, 539-556.
    • (1985) Mol. Biol. Evol. , vol.2 , pp. 539-556
    • Stephens, J.C.1
  • 23
    • 0026644652 scopus 로고
    • Sequence diversity within the argF, fbp and recA genes of natural isolates of Neisseria meningitidis: Interspecies recombination within the argf gene
    • Zhou, J. and Spratt, B.G. (1992) Sequence diversity within the argF, fbp and recA genes of natural isolates of Neisseria meningitidis: interspecies recombination within the argf gene. Mol. Microbiol., 6, 2135-2146.
    • (1992) Mol. Microbiol. , vol.6 , pp. 2135-2146
    • Zhou, J.1    Spratt, B.G.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.