메뉴 건너뛰기




Volumn 23, Issue 2, 2007, Pages

Phylogeny reconstruction: Increasing the accuracy of pairwise distance estimation using Bayesian inference of evolutionary rates

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; AMINO ACID SEQUENCE; BAYES THEOREM; COMPUTER SIMULATION; CONFERENCE PAPER; EVOLUTIONARY RATE; GENETIC DATABASE; GENETIC DISTANCE; INFORMATION RETRIEVAL; MATHEMATICAL ANALYSIS; PHYLOGENY; PRIORITY JOURNAL; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; STATISTICAL MODEL;

EID: 33846691679     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btl304     Document Type: Conference Paper
Times cited : (11)

References (24)
  • 1
    • 0035838976 scopus 로고    scopus 로고
    • Automated structure-based prediction of functional sites in proteins: Applications to assessing the validity of inheriting protein function from homology in genome annotation and to protein docking
    • Aloy,P. et al. (2001) Automated structure-based prediction of functional sites in proteins: Applications to assessing the validity of inheriting protein function from homology in genome annotation and to protein docking. J. Mol. Biol., 311(2), 395-408.
    • (2001) J. Mol. Biol. , vol.311 , Issue.2 , pp. 395-408
    • Aloy, P.1
  • 2
    • 0030801002 scopus 로고    scopus 로고
    • Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
    • Altschul,S.F. et al. (1997) Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res, 25(17), 3389-3402.
    • (1997) Nucleic Acids Res , vol.25 , Issue.17 , pp. 3389-3402
    • Altschul, S.F.1
  • 3
    • 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
  • 4
    • 0003991673 scopus 로고    scopus 로고
    • Sinauer Associates, Sunderland, Massachusetts
    • Felsenstein,J. et al. (2004) Inferring Phylogenies. Sinauer Associates, Sunderland, Massachusetts.
    • (2004) Inferring Phylogenies
    • Felsenstein, J.1
  • 5
    • 0036110773 scopus 로고    scopus 로고
    • A structural EM algorithm for phylogenetic inference
    • Friedman,N. (2002) A structural EM algorithm for phylogenetic inference. J Comput Biol, 9(2), 331-353.
    • (2002) J Comput Biol , vol.9 , Issue.2 , pp. 331-353
    • Friedman, N.1
  • 6
    • 0026099641 scopus 로고
    • Robustness of maximum likelihood tree estimation against different patterns of base substitutions
    • Fukami-Kobayashi,K. and Tateno,Y. (1991) Robustness of maximum likelihood tree estimation against different patterns of base substitutions. J Mol Evol, 32(l), 79-91.
    • (1991) J Mol Evol , vol.32 , Issue.1 , pp. 79-91
    • Fukami-Kobayashi, K.1    Tateno, Y.2
  • 7
    • 0242578620 scopus 로고    scopus 로고
    • A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood
    • Guindon,S. and Gascuel,O. (2003) A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol., 52(5), 696-704.
    • (2003) Syst. Biol. , vol.52 , Issue.5 , pp. 696-704
    • Guindon, S.1    Gascuel, O.2
  • 8
    • 0027565033 scopus 로고
    • Relative efficiencies of the maximum likelihood, maximum parsimony, and neighbor-joining methods for estimating protein phylogeny
    • Hasegawa,M. and Fujiwara,M. (1993) Relative efficiencies of the maximum likelihood, maximum parsimony, and neighbor-joining methods for estimating protein phylogeny. Mol Phylogenet Evol, 2(1), 1-5.
    • (1993) Mol Phylogenet Evol , vol.2 , Issue.1 , pp. 1-5
    • Hasegawa, M.1    Fujiwara, M.2
  • 9
    • 0029113744 scopus 로고
    • The robustness of two phylogenetic methods: Four-taxon simulations reveal a slight superiority of maximum likelihood over neighbor joining
    • Huelsenbeck,J.P. (1995) The robustness of two phylogenetic methods: four-taxon simulations reveal a slight superiority of maximum likelihood over neighbor joining. Mol Biol Evol, 12(5), 843-849.
    • (1995) Mol Biol Evol , vol.12 , Issue.5 , pp. 843-849
    • Huelsenbeck, J.P.1
  • 10
    • 0032746022 scopus 로고    scopus 로고
    • Disk-covering, a fast-converging method for phylogenetic tree reconstruction
    • Huson,D.H. et al. (1999) Disk-covering, a fast-converging method for phylogenetic tree reconstruction. Journal of Computational Biology, 6(3-4), 369-386.
    • (1999) Journal of Computational Biology , vol.6 , Issue.3-4 , pp. 369-386
    • Huson, D.H.1
  • 11
    • 0026691182 scopus 로고
    • The rapid generation of mutation data matrices from protein sequences
    • Jones,D.T. et al. (1992) The rapid generation of mutation data matrices from protein sequences. Computer Applications in the Biosciences, 8, 275-282.
    • (1992) Computer Applications in the Biosciences , vol.8 , pp. 275-282
    • Jones, D.T.1
  • 12
    • 0000732090 scopus 로고
    • Evolution of protein molecules
    • In H.N. Munro, editor, Academic Press, New York
    • Jukes,T.H. and Cantor,C.R. (1969) Evolution of protein molecules. In H.N. Munro, editor, Mammalian protein metabolism, pp. 21-132. Academic Press, New York.
    • (1969) Mammalian Protein Metabolism , pp. 21-132
    • Jukes, T.H.1    Cantor, C.R.2
  • 14
    • 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
  • 15
    • 0028177080 scopus 로고
    • A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates
    • Kuhner,M.K. and Felsenstein,J. (1994) A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates. Mol Biol Evol, 11(3), 459-468.
    • (1994) Mol Biol Evol , vol.11 , Issue.3 , pp. 459-468
    • Kuhner, M.K.1    Felsenstein, J.2
  • 16
    • 4143051195 scopus 로고    scopus 로고
    • Comparison of Site-Specific Rate-Inference Methods for Protein Sequences: Empirical Bayesian Methods Are Superior
    • Mayrose,I. et al. (2004) Comparison of Site-Specific Rate-Inference Methods for Protein Sequences: Empirical Bayesian Methods Are Superior. Mol Biol Evol, 21(9), 1781-1791.
    • (2004) Mol Biol Evol , vol.21 , Issue.9 , pp. 1781-1791
    • Mayrose, I.1
  • 17
    • 0031153858 scopus 로고    scopus 로고
    • Site-by-site estimation of the rate of substitution and the correlation of rates in mitochondrial DNA
    • Nielsen,R. (1997) Site-by-site estimation of the rate of substitution and the correlation of rates in mitochondrial DNA. Syst Biol, 46(2), 346-353.
    • (1997) Syst Biol , vol.46 , Issue.2 , pp. 346-353
    • Nielsen, R.1
  • 18
    • 0002218484 scopus 로고    scopus 로고
    • Rate4Site: An algorithmic tool for the identification of functional regions in proteins by surface mapping of evolutionary determinants within their homologues
    • Pupko,T. (2002) Rate4Site: An algorithmic tool for the identification of functional regions in proteins by surface mapping of evolutionary determinants within their homologues. Bioinformatics, 18(Suppl 1), pp. 71-77.
    • (2002) Bioinformatics , vol.18 , Issue.SUPPL. 1 , pp. 71-77
    • Pupko, T.1
  • 19
    • 0023375195 scopus 로고
    • The neighbor-joining method: A new method for reconstructing phylogenetic trees
    • Saitou,N. and Nei,M. (1987) The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol Biol Evol, 4(4), 406-425.
    • (1987) Mol Biol Evol , vol.4 , Issue.4 , pp. 406-425
    • Saitou, N.1    Nei, M.2
  • 20
    • 19544387609 scopus 로고    scopus 로고
    • Evaluating the performance of a successive-approximations approach to parameter optimization in maximum-likelihood phylogeny estimation
    • Sullivan,J. et al. (2005) Evaluating the performance of a successive-approximations approach to parameter optimization in maximum-likelihood phylogeny estimation. Mol Biol Evol, 22(6), 1386-1392.
    • (2005) Mol Biol Evol , vol.22 , Issue.6 , pp. 1386-1392
    • Sullivan, J.1
  • 21
    • 0028205953 scopus 로고
    • Relative efficiencies of the maximum-likelihood, neighbor-joining, and maximum-parsimony methods when substitution rate varies with site
    • Tateno,Y. et al. (1994) Relative efficiencies of the maximum-likelihood, neighbor-joining, and maximum-parsimony methods when substitution rate varies with site. Mol Biol Evol, 11(2), 261-277.
    • (1994) Mol Biol Evol , vol.11 , Issue.2 , pp. 261-277
    • Tateno, Y.1
  • 22
    • 0028064845 scopus 로고
    • Maximum likelihood phylogenetic estimation from dna sequences with variable rates over sites: Approximate methods
    • Yang,Z. (1994) Maximum likelihood phylogenetic estimation from dna sequences with variable rates over sites: Approximate methods. J Mol Evol, 39(3), 306-314.
    • (1994) J Mol Evol , vol.39 , Issue.3 , pp. 306-314
    • Yang, Z.1
  • 23
    • 0030451420 scopus 로고    scopus 로고
    • Among-site rate variation and its impact on phylogenetic analyses
    • Yang,Z. (1996) Among-site rate variation and its impact on phylogenetic analyses. Trends Ecol. Evol., 11, 367-372.
    • (1996) Trends Ecol. Evol. , vol.11 , pp. 367-372
    • Yang, Z.1
  • 24
    • 0028108336 scopus 로고
    • Estimation of evolutionary distances between nucleotide sequences
    • Zharkikh,A. (1994) Estimation of evolutionary distances between nucleotide sequences. J. Mol. Evol., 39(3), 315-329.
    • (1994) J. Mol. Evol. , vol.39 , Issue.3 , pp. 315-329
    • Zharkikh, A.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.