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Volumn 147, Issue 1, 2010, Pages 47-52

Effects of methodology and analysis strategy on robustness of pestivirus phylogeny

Author keywords

Bayesian approach; Classification; Maximum likelihood; Maximum parsimony; Pestivirus; Phylogeny

Indexed keywords

5' UNTRANSLATED REGION; ARTICLE; BAYES THEOREM; GENE SEQUENCE; MAXIMUM LIKELIHOOD METHOD; NEIGHBOR JOINING METHOD; NONHUMAN; NUCLEOTIDE SEQUENCE; PARSIMONY ANALYSIS; PESTIVIRUS; PHYLOGENY; PRIORITY JOURNAL; UNINDEXED SEQUENCE; VIRAL GENETICS; VIRUS CLASSIFICATION;

EID: 71149120980     PISSN: 01681702     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.virusres.2009.10.004     Document Type: Article
Times cited : (13)

References (39)
  • 2
    • 0031371067 scopus 로고    scopus 로고
    • Multiple sources of character information and the phylogeny of Hawaiian drosophilids
    • Baker R.H., and DeSalle R. Multiple sources of character information and the phylogeny of Hawaiian drosophilids. Syst. Biol. 46 (1997) 654-673
    • (1997) Syst. Biol. , vol.46 , pp. 654-673
    • Baker, R.H.1    DeSalle, R.2
  • 4
    • 0033568074 scopus 로고    scopus 로고
    • Genetic diversity of pestiviruses: identification of novel groups and implications for classification
    • Becher P., Orlich M., Kosmidou A., Konig M., Baroth M., and Thiel H.-J. Genetic diversity of pestiviruses: identification of novel groups and implications for classification. Virology 262 (1999) 64-71
    • (1999) Virology , vol.262 , pp. 64-71
    • Becher, P.1    Orlich, M.2    Kosmidou, A.3    Konig, M.4    Baroth, M.5    Thiel, H.-J.6
  • 7
    • 0032805771 scopus 로고    scopus 로고
    • Corroboration among data sets in simultaneous analysis: hidden support for phylogenetic relationships among higher level artiodactyl taxa
    • Gatesy J., O'Grady P., and Baker R.H. Corroboration among data sets in simultaneous analysis: hidden support for phylogenetic relationships among higher level artiodactyl taxa. Cladistics 15 (1999) 271-313
    • (1999) Cladistics , vol.15 , pp. 271-313
    • Gatesy, J.1    O'Grady, P.2    Baker, R.H.3
  • 8
    • 0033499153 scopus 로고    scopus 로고
    • Analyzing large data sets in reasonable times: solutions for composite optima
    • Goloboff P.A. Analyzing large data sets in reasonable times: solutions for composite optima. Cladistics 15 (1999) 415-428
    • (1999) Cladistics , vol.15 , pp. 415-428
    • Goloboff, P.A.1
  • 9
    • 45749124657 scopus 로고    scopus 로고
    • TNT, a free program for phylogenetic analysis
    • Goloboff P.A., Farris J.S., and Nixon K.C. TNT, a free program for phylogenetic analysis. Cladistics 24 (2008) 774-786
    • (2008) Cladistics , vol.24 , pp. 774-786
    • Goloboff, P.A.1    Farris, J.S.2    Nixon, K.C.3
  • 10
    • 0242578620 scopus 로고    scopus 로고
    • A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood
    • Guindon S., and Gascuel O. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52 (2003) 696-704
    • (2003) Syst. Biol. , vol.52 , pp. 696-704
    • Guindon, S.1    Gascuel, O.2
  • 11
    • 33751253784 scopus 로고    scopus 로고
    • Recombination patterns in aphthoviruses mirror those found in other picornaviruses
    • Heath L., van der Walt E., Varsani A., and Martin D.P. Recombination patterns in aphthoviruses mirror those found in other picornaviruses. J. Virol. 80 (2006) 11827-11832
    • (2006) J. Virol. , vol.80 , pp. 11827-11832
    • Heath, L.1    van der Walt, E.2    Varsani, A.3    Martin, D.P.4
  • 12
    • 0028189715 scopus 로고
    • Rapid characterization of new pestivirus strains by direct sequencing of PCR-amplified cDNA from the 5′ noncoding region
    • Hofmann M.A., Brechtbühl K., and Stäuber N. Rapid characterization of new pestivirus strains by direct sequencing of PCR-amplified cDNA from the 5′ noncoding region. Arch. Virol. 139 (1994) 217-229
    • (1994) Arch. Virol. , vol.139 , pp. 217-229
    • Hofmann, M.A.1    Brechtbühl, K.2    Stäuber, N.3
  • 13
    • 0037379673 scopus 로고    scopus 로고
    • Phylogeny estimation: traditional and Bayesian approaches
    • Holder M., and Lewis P.O. Phylogeny estimation: traditional and Bayesian approaches. Nat. Rev. Genet. 4 (2003) 275-284
    • (2003) Nat. Rev. Genet. , vol.4 , pp. 275-284
    • Holder, M.1    Lewis, P.O.2
  • 14
    • 0034849408 scopus 로고    scopus 로고
    • MRBAYES: Bayesian inference of phylogenetic trees
    • Huelsenbeck J.P., and Ronquist F. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17 (2001) 754-755
    • (2001) Bioinformatics , vol.17 , pp. 754-755
    • Huelsenbeck, J.P.1    Ronquist, F.2
  • 15
    • 11144245282 scopus 로고    scopus 로고
    • Phylogenetic analysis of bovine pestiviruses: testing the evolution of clinical symptoms
    • Jones L.R., Cigliano M.M., Zandomeni R.O., and Weber E.L. Phylogenetic analysis of bovine pestiviruses: testing the evolution of clinical symptoms. Cladistics 20 (2004) 443-453
    • (2004) Cladistics , vol.20 , pp. 443-453
    • Jones, L.R.1    Cigliano, M.M.2    Zandomeni, R.O.3    Weber, E.L.4
  • 16
    • 0019296687 scopus 로고
    • A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences
    • Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 16 (1980) 111-120
    • (1980) J. Mol. Evol. , vol.16 , pp. 111-120
    • Kimura, M.1
  • 17
    • 34748873170 scopus 로고    scopus 로고
    • Flaviviridae: the viruses and their replication
    • Knipe D.M., and Howley P.M. (Eds), Lippincott-Raven, Philadelphia, PA
    • Lindenbach B.D., Thiel H.-J., and Rice C.M. Flaviviridae: the viruses and their replication. In: Knipe D.M., and Howley P.M. (Eds). Fields Virology. 5th ed. vol. 1 (2007), Lippincott-Raven, Philadelphia, PA 1101-1152
    • (2007) Fields Virology. 5th ed. , vol.1 , pp. 1101-1152
    • Lindenbach, B.D.1    Thiel, H.-J.2    Rice, C.M.3
  • 18
    • 66649105171 scopus 로고    scopus 로고
    • Virus recovery and full-length sequence analysis of the atypical bovine pestivirus Th/04_KhonKaen
    • Liu L., Kampa J., Belák S., and Baule C. Virus recovery and full-length sequence analysis of the atypical bovine pestivirus Th/04_KhonKaen. Vet. Microbiol. 138 (2009) 62-68
    • (2009) Vet. Microbiol. , vol.138 , pp. 62-68
    • Liu, L.1    Kampa, J.2    Belák, S.3    Baule, C.4
  • 19
    • 60649116779 scopus 로고    scopus 로고
    • Phylogeny, classification and evolutionary insights into pestiviruses
    • Liu L., Xia H., Wahlberg N., Belák S., and Baule C. Phylogeny, classification and evolutionary insights into pestiviruses. Virology 385 (2009) 351-357
    • (2009) Virology , vol.385 , pp. 351-357
    • Liu, L.1    Xia, H.2    Wahlberg, N.3    Belák, S.4    Baule, C.5
  • 20
    • 0029933684 scopus 로고    scopus 로고
    • Classical swine fever virus diversity and evolution
    • Lowings P., Ibata G., Needham J., and Paton D. Classical swine fever virus diversity and evolution. J. Gen. Virol. 77 (1996) 1311-1321
    • (1996) J. Gen. Virol. , vol.77 , pp. 1311-1321
    • Lowings, P.1    Ibata, G.2    Needham, J.3    Paton, D.4
  • 21
    • 0032810549 scopus 로고    scopus 로고
    • Searching for most parsimonious trees with simulated evolutionary optimization
    • Moilanen A. Searching for most parsimonious trees with simulated evolutionary optimization. Cladistics 15 (1999) 39-50
    • (1999) Cladistics , vol.15 , pp. 39-50
    • Moilanen, A.1
  • 22
    • 39049114551 scopus 로고    scopus 로고
    • Identification of new genetic subtypes of bovine viral diarrhea virus genotype 1 isolated in Japan
    • Nagai M., Hayashi M., Itou M., Fukutomi T., Akashi H., Kida H., and Sakoda Y. Identification of new genetic subtypes of bovine viral diarrhea virus genotype 1 isolated in Japan. Virus Genes 36 (2008) 135-139
    • (2008) Virus Genes , vol.36 , pp. 135-139
    • Nagai, M.1    Hayashi, M.2    Itou, M.3    Fukutomi, T.4    Akashi, H.5    Kida, H.6    Sakoda, Y.7
  • 24
    • 0033504552 scopus 로고    scopus 로고
    • The parsimony ratchet, a new method for rapid parsimony analysis
    • Nixon K.C. The parsimony ratchet, a new method for rapid parsimony analysis. Cladistics 15 (1999) 407-414
    • (1999) Cladistics , vol.15 , pp. 407-414
    • Nixon, K.C.1
  • 26
    • 0027953871 scopus 로고
    • Identification of a new group of bovine viral diarrhea virus strains associated with severe outbreaks and high mortalities
    • Pellerin C., van den Hurk J., Lecomte J., and Tussen P. Identification of a new group of bovine viral diarrhea virus strains associated with severe outbreaks and high mortalities. Virology 203 (1994) 260-268
    • (1994) Virology , vol.203 , pp. 260-268
    • Pellerin, C.1    van den Hurk, J.2    Lecomte, J.3    Tussen, P.4
  • 28
    • 0027949184 scopus 로고
    • Segregation of bovine viral diarrhea virus into genotypes
    • Ridpath J.F., Bolin S.R., and Dubovi E.J. Segregation of bovine viral diarrhea virus into genotypes. Virology 205 (1994) 66-74
    • (1994) Virology , vol.205 , pp. 66-74
    • Ridpath, J.F.1    Bolin, S.R.2    Dubovi, E.J.3
  • 29
    • 0041386108 scopus 로고    scopus 로고
    • MrBayes 3: Bayesian phylogenetic inference under mixed models
    • Ronquist F., and Huelsenbeck J.P. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19 (2003) 1572-1574
    • (2003) Bioinformatics , vol.19 , pp. 1572-1574
    • Ronquist, F.1    Huelsenbeck, J.P.2
  • 30
    • 60649116776 scopus 로고    scopus 로고
    • Molecular biology of pestiviruses
    • Mettenleiter T.C., and Sobrino F. (Eds), Caister Academic Press, Norfolk, UK
    • Rümenapf T., and Thiel H.-J. Molecular biology of pestiviruses. In: Mettenleiter T.C., and Sobrino F. (Eds). Animal Viruses: Molecular Biology (2008), Caister Academic Press, Norfolk, UK 39-96
    • (2008) Animal Viruses: Molecular Biology , pp. 39-96
    • Rümenapf, T.1    Thiel, H.-J.2
  • 31
    • 9944248535 scopus 로고    scopus 로고
    • Genetic and antigenic characterization of an atypical pestivirus isolate, a putative member of a novel pestivirus species
    • Schirrmeier H., Strebelow G., Depner K., Hoffmann B., and Beer M. Genetic and antigenic characterization of an atypical pestivirus isolate, a putative member of a novel pestivirus species. J. Gen. Virol. 85 (2004) 3647-3652
    • (2004) J. Gen. Virol. , vol.85 , pp. 3647-3652
    • Schirrmeier, H.1    Strebelow, G.2    Depner, K.3    Hoffmann, B.4    Beer, M.5
  • 33
    • 0026711010 scopus 로고
    • Estimation of the number of nucleotide substitutions when there are strong transition-transversion and G + C-content biases
    • Tamura K. Estimation of the number of nucleotide substitutions when there are strong transition-transversion and G + C-content biases. Mol. Biol. Evol. 9 (1992) 678-687
    • (1992) Mol. Biol. Evol. , vol.9 , pp. 678-687
    • Tamura, K.1
  • 34
    • 34547781750 scopus 로고    scopus 로고
    • MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0
    • Tamura K., Dudley J., Nei M., and Kumar S. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol. Biol. Evol. 24 (2007) 1596-1599
    • (2007) Mol. Biol. Evol. , vol.24 , pp. 1596-1599
    • Tamura, K.1    Dudley, J.2    Nei, M.3    Kumar, S.4
  • 36
    • 0027968068 scopus 로고
    • CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
    • Thompson J.D., Higgins D.G., and Gibson T.J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22 (1994) 4673-4680
    • (1994) Nucleic Acids Res. , vol.22 , pp. 4673-4680
    • Thompson, J.D.1    Higgins, D.G.2    Gibson, T.J.3
  • 39
    • 35748939384 scopus 로고    scopus 로고
    • Molecular phylogenetic analysis of bovine viral diarrhoea virus: a Bayesian approach
    • Xia H., Liu L., Wahlberg N., Baule C., and Belák S. Molecular phylogenetic analysis of bovine viral diarrhoea virus: a Bayesian approach. Virus Res. 137 (2007) 53-62
    • (2007) Virus Res. , vol.137 , pp. 53-62
    • Xia, H.1    Liu, L.2    Wahlberg, N.3    Baule, C.4    Belák, S.5


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