메뉴 건너뛰기




Volumn , Issue , 2006, Pages

PBPI: A high performance implementation of Bayesian phylogenetic inference

Author keywords

[No Author keywords available]

Indexed keywords

LIKELIHOOD-BASED ASSESSMENT; PHYLOGENETIC INFERENCE; STATISTIC MODELS;

EID: 34548252486     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1145/1188455.1188535     Document Type: Conference Paper
Times cited : (29)

References (34)
  • 3
    • 0036806280 scopus 로고    scopus 로고
    • Potential applications and pitfalls of Bayesian inference of phylogeny
    • Huelsenbeck, J. P., Larget, B., Miller, R. E., et al., "Potential applications and pitfalls of Bayesian inference of phylogeny," Syst. Biol., vol. 51, pp. 673-688, 2002.
    • (2002) Syst. Biol , vol.51 , pp. 673-688
    • Huelsenbeck, J.P.1    Larget, B.2    Miller, R.E.3
  • 4
    • 0035861441 scopus 로고    scopus 로고
    • Resolution of the Early Placental Mammal Radiation Using Bayesian Phylogenetics
    • Murphy, W. J., Eizirik, E., O'brien, S. J., et al., "Resolution of the Early Placental Mammal Radiation Using Bayesian Phylogenetics," Science, vol. 294, pp. 2348-2351, 2001.
    • (2001) Science , vol.294 , pp. 2348-2351
    • Murphy, W.J.1    Eizirik, E.2    O'brien, S.J.3
  • 5
    • 4544296370 scopus 로고    scopus 로고
    • Bayesian inference of the metazoan phylogeny: A combined molecular and morphological approach
    • Glenner, H., Hansen, A. J., Sorensen, M. V., et al., "Bayesian inference of the metazoan phylogeny: A combined molecular and morphological approach," Current Biology, vol. 14, pp. 1644-1649, 2004.
    • (2004) Current Biology , vol.14 , pp. 1644-1649
    • Glenner, H.1    Hansen, A.J.2    Sorensen, M.V.3
  • 7
    • 0034849408 scopus 로고    scopus 로고
    • MRBAYES: Bayesian inference of phylogenetic trees
    • Huelsenbeck, J. P. and Ronquist, F., "MRBAYES: Bayesian inference of phylogenetic trees," Bioinformatics, vol. 17, pp. 754-755, 2001.
    • (2001) Bioinformatics , vol.17 , pp. 754-755
    • Huelsenbeck, J.P.1    Ronquist, F.2
  • 8
    • 5744249209 scopus 로고
    • Equations of state calculations by fast computing machine
    • Metropolis, N., Rosenbluth, A. N., Rosenbluth, M. N., et al., "Equations of state calculations by fast computing machine," J. Chem. Phys., vol. 21, pp. 1087-1091, 1953.
    • (1953) J. Chem. Phys , vol.21 , pp. 1087-1091
    • Metropolis, N.1    Rosenbluth, A.N.2    Rosenbluth, M.N.3
  • 9
    • 77956890234 scopus 로고
    • Monte Carlo sampling methods using Markov chains and their application
    • Hastings, W. K., "Monte Carlo sampling methods using Markov chains and their application," Biometrika, vol. 57, pp. 97-109, 1970.
    • (1970) Biometrika , vol.57 , pp. 97-109
    • Hastings, W.K.1
  • 10
    • 0021518209 scopus 로고
    • Stochastic Relaxation, Gibbs Distributions, and the Bayesian Restoration of Images
    • Geman, S. and Geman, D., "Stochastic Relaxation, Gibbs Distributions, and the Bayesian Restoration of Images," IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 6, pp. 721-741, 1984.
    • (1984) IEEE Transactions on Pattern Analysis and Machine Intelligence , vol.6 , pp. 721-741
    • Geman, S.1    Geman, D.2
  • 11
    • 0000576595 scopus 로고
    • Markov-Chains for Exploring Posterior Distributions
    • Tierney, L., "Markov-Chains for Exploring Posterior Distributions," Annals of Statistics, vol. 22, pp. 1701-1728, 1994.
    • (1994) Annals of Statistics , vol.22 , pp. 1701-1728
    • Tierney, L.1
  • 12
    • 0019797407 scopus 로고
    • Evolutionary trees from DNA sequences: A maximum likelihood approach
    • Felsenstein, J., "Evolutionary trees from DNA sequences: a maximum likelihood approach," Journal of Molecular Evolution, vol. 17, pp. 368-76, 1981.
    • (1981) Journal of Molecular Evolution , vol.17 , pp. 368-376
    • Felsenstein, J.1
  • 15
    • 34548291608 scopus 로고    scopus 로고
    • High Performance, Bayesian-based Phylogenetic Inference Framework,
    • PhD Dissertation, Department of Computer Science and Engineering, University of South Carolina
    • Feng, X., "High Performance, Bayesian-based Phylogenetic Inference Framework," PhD Dissertation, Department of Computer Science and Engineering, University of South Carolina, 2006.
    • (2006)
    • Feng, X.1
  • 16
    • 13444304367 scopus 로고    scopus 로고
    • The Ribosomal Database Project (RDP-II): Sequences and tools for high-throughput rRNA analysis
    • Cole, J. R., Chai, B., Farris, R. J., et al., "The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysis," Nucl. Acids Res., vol. 33, pp. D294-296, 2005.
    • (2005) Nucl. Acids Res , vol.33
    • Cole, J.R.1    Chai, B.2    Farris, R.J.3
  • 17
    • 0030928378 scopus 로고    scopus 로고
    • Seq-Gen: An application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic frees
    • Rambaut, A. and Grassly, N. C., "Seq-Gen: An application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic frees," Computer Applications in the Biosciences, vol. 13, pp. 235-238, 1997.
    • (1997) Computer Applications in the Biosciences , vol.13 , pp. 235-238
    • Rambaut, A.1    Grassly, N.C.2
  • 18
    • 85060036181 scopus 로고
    • Validity of the Single Processor Approach to Achieving Large-Scale Computing Capabilities
    • Reston, VA
    • Amdahl, G. M., "Validity of the Single Processor Approach to Achieving Large-Scale Computing Capabilities," in Proceedings of AFIPS Spring Joint Computer Conference, Reston, VA, 1967.
    • (1967) Proceedings of AFIPS Spring Joint Computer Conference
    • Amdahl, G.M.1
  • 19
    • 0024012163 scopus 로고
    • Reevaluating Amdahl's Law
    • Gustafson, J., "Reevaluating Amdahl's Law," Communications of the Acm, vol. 31, pp. 532-533, 1988.
    • (1988) Communications of the Acm , vol.31 , pp. 532-533
    • Gustafson, J.1
  • 20
    • 0030749810 scopus 로고    scopus 로고
    • Bayesian phylogenetic inference using DNA sequences: A Markov Chain Monte Carlo method
    • Yang, Z. H. and Rannala, B., "Bayesian phylogenetic inference using DNA sequences: A Markov Chain Monte Carlo method," Molecular Biology and Evolution, vol. 14, pp. 717-724, 1997.
    • (1997) Molecular Biology and Evolution , vol.14 , pp. 717-724
    • Yang, Z.H.1    Rannala, B.2
  • 21
    • 0032906031 scopus 로고    scopus 로고
    • Bayesian phylogenetic inference via Markov chain Monte Carlo methods
    • Mau, B., Newton, M. A., and Larget, B., "Bayesian phylogenetic inference via Markov chain Monte Carlo methods," Biometrics, vol. 55, pp. 1-12, 1999.
    • (1999) Biometrics , vol.55 , pp. 1-12
    • Mau, B.1    Newton, M.A.2    Larget, B.3
  • 24
    • 0035861456 scopus 로고    scopus 로고
    • Bayesian inference of phylogeny and its impact on evolutionary biology
    • Huelsenbeck, J., Ronquist, F., Nielsen, R., et al., "Bayesian inference of phylogeny and its impact on evolutionary biology," Science, vol. 294, pp. 2310-2314, 2001.
    • (2001) Science , vol.294 , pp. 2310-2314
    • Huelsenbeck, J.1    Ronquist, F.2    Nielsen, R.3
  • 25
    • 0037379673 scopus 로고    scopus 로고
    • Phylogeny estimation: Traditional and Bayesian approaches
    • Holder, M. and Lewis, P. O., "Phylogeny estimation: traditional and Bayesian approaches," Nature Rev. Genet., vol. 4, pp. 275-284, 2003.
    • (2003) Nature Rev. Genet , vol.4 , pp. 275-284
    • Holder, M.1    Lewis, P.O.2
  • 26
    • 1342309210 scopus 로고    scopus 로고
    • Parallel metropolis coupled Markov chain Monte Carlo for Bayesian phylogenetic inference
    • Altekar, G., Dwarkadas, S., Huelsenbeck, J. P., et al., "Parallel metropolis coupled Markov chain Monte Carlo for Bayesian phylogenetic inference," Bioinformatics, vol. 20, pp. 407-415, 2004.
    • (2004) Bioinformatics , vol.20 , pp. 407-415
    • Altekar, G.1    Dwarkadas, S.2    Huelsenbeck, J.P.3
  • 28
    • 0027957393 scopus 로고
    • fastDNAmL: A tool for construction of phylogenetic trees of DNA sequences using maximum likelihood
    • Olsen, G., Matsuda, H., Hagstrom, R., et al., "fastDNAmL: a tool for construction of phylogenetic trees of DNA sequences using maximum likelihood," Comput. Appl. Biosci., vol. 10, pp. 41-48, 1994.
    • (1994) Comput. Appl. Biosci , vol.10 , pp. 41-48
    • Olsen, G.1    Matsuda, H.2    Hagstrom, R.3
  • 29
    • 14644397888 scopus 로고    scopus 로고
    • RAxML-III: A fast program for maximum likelihood-based inference of large phylogenetic trees
    • Stamatakis, A., Ludwig, T., and Meier, H., "RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees," Bioinformatics, vol. 21, pp. 456-463, 2005.
    • (2005) Bioinformatics , vol.21 , pp. 456-463
    • Stamatakis, A.1    Ludwig, T.2    Meier, H.3
  • 30
    • 0036790011 scopus 로고    scopus 로고
    • Genetic algorithms and parallel processing in maximum-likelihood phylogeny inference
    • Brauer, M. J., Holder, M. T., Dries, L. A., et al., "Genetic algorithms and parallel processing in maximum-likelihood phylogeny inference," Molecular Biology and Evolution, vol. 19, pp. 1717-1726, 2002.
    • (2002) Molecular Biology and Evolution , vol.19 , pp. 1717-1726
    • Brauer, M.J.1    Holder, M.T.2    Dries, L.A.3
  • 31
    • 0036205377 scopus 로고    scopus 로고
    • TREE-PUZZLE: Maximum likelihood phylogenetic analysis using quartets and parallel computing
    • Schmidt, H. A., Strimmer, K., Vingron, M., et al., "TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing," Bioinformatics, vol. 18, pp. 502-504, 2002.
    • (2002) Bioinformatics , vol.18 , pp. 502-504
    • Schmidt, H.A.1    Strimmer, K.2    Vingron, M.3
  • 32
    • 0036568578 scopus 로고    scopus 로고
    • High-performance algorithm engineering for computational phylogenetics
    • Moret, B. M. E., Bader, D. A., and Warnow, T., "High-performance algorithm engineering for computational phylogenetics," Journal of Supercomputing, vol. 22, pp. 99-110, 2002.
    • (2002) Journal of Supercomputing , vol.22 , pp. 99-110
    • Moret, B.M.E.1    Bader, D.A.2    Warnow, T.3
  • 33
    • 0032030505 scopus 로고    scopus 로고
    • Phylogenetic supertrees: Assembling the trees of life
    • Sanderson, M. J., Purvis, A., and Henze, C., "Phylogenetic supertrees: assembling the trees of life," Trends in Ecology & Evolution, vol. 13, pp. 105-109, 1998.
    • (1998) Trends in Ecology & Evolution , vol.13 , pp. 105-109
    • Sanderson, M.J.1    Purvis, A.2    Henze, C.3
  • 34
    • 0032746022 scopus 로고    scopus 로고
    • Disk-covering, a fast-converging method for phylogenetic tree reconstruction
    • Huson, D. H., Nettles, S. M., and Warnow, T. J., "Disk-covering, a fast-converging method for phylogenetic tree reconstruction," Journal of Computational Biology, vol. 6, pp. 369-386, 1999.
    • (1999) Journal of Computational Biology , vol.6 , pp. 369-386
    • Huson, D.H.1    Nettles, S.M.2    Warnow, T.J.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.