A generalized Markov sampler

Methodology and Computing in Applied Probability

Volumn 6, Issue 1, 2004, Pages 29-53

  Keith, Jonathan M ^a   Kroese, Dirk P ^a   Bryant, Darryn ^a  

^a UNIVERSITY OF QUEENSLAND   (Australia)

Author keywords

Consensus sequence; Gibbs sampler; Isochores; Markov chain Monte Carlo; Model determination; Multiple change point analysis; Phylogenetic inference; Simulated annealing; String sampler

Indexed keywords

EID: 7244220822     PISSN: 13875841     EISSN: None     Source Type: Journal    
DOI: 10.1023/B:MCAP.0000012414.14405.15     Document Type: Review

References (20)

1. A. A. Barker, "Monte Carlo calculations of the radial distribution functions for a proton-electron plasma," Aust. J. Phys. vol. 18 pp. 119-133, 1965.
2. B. P. Carlin and S. Chib "Bayesian model choice via MCMC," J. Royal Statist. Society series B.57 pp. 473-484, 1995.
3. W. M. Fitch, "Toward defining the course of evolution: minimum change for a specific tree topology," Syst. Zool. vol. 20 pp. 406-416, 1971.
4. A. F. Gelfand and A. F. M. Smith, "Sampling-based approaches to calculating marginal densities," J. Am. Stat. Assoc. vol. 85 pp. 398-409, 1990.
5. S. Geman and D. Geman, "Stochastic relaxation, Gibbs distributions, and the Bayesian restoration of images," IEEE T. Pattern Anal. vol. 6 pp. 721-741, 1984.
6. P. J. Green, "Reversible jump Markov chain Monte Carlo computation and Bayesian model determination," Biometrika vol. 82 pp. 711-732, 1995.
7. W. K. Hastings, "Monte Carlo sampling methods using Markov chains and their applications," Biometrika vol. 57 pp. 97-109, 1970.
8. J. P. Huelsenbeck and F. Ronquist, "Mr Bayes: Bayesian inference of phylogenetic trees," Bioinformatics vol. 17 pp. 754-755, 2001.
9. International Human Genome Sequencing Consortium, "Initial sequencing and analysis of the human genome," Nature vol. 409 pp. 860-921, 2001.
10. J. M. Keith, P. Adams, D. Bryant, D. P. Kroese, K. R. Mitchelson, D. A. E. Cochran, and G. H. Lala, "A simulated annealing algorithm for finding consensus sequences," Bioinformatics vol. 18 pp. 1494-1499, 2002.
11. J. M. Keith, P. Adams, D. Bryant, K. R. Mitchelson, D. A. E. Cochran, and G. H. Lala, "Inferring an original sequence from erroneous copies: a Bayesian approach," in Yi-Ping Phoebe Chen (ed.), Proceedings of the 1st Asia-Pacific Bioinformatics Conference (APBC2003), Conferences in Research and Practice in Information Technology, vol. 19 pp. 23-28, 2003a.
12. J. M. Keith, P. Adams, D. Bryant, K. R. Mitchelson, D. A. E. Cochran, and G. H. Lala, "Inferring an original sequence from erroneous copies: two approaches," Asia-Pacific BioTech News vol. 7 pp. 107-114, 2003.
13. B. Larget and D. Simon, "Markov chain Monte Carlo algorithms for the Bayesian analysis of phylogenetic trees," Mol. Biol. Evol. vol. 16 pp. 750-759, 1999.
14. B. Mau and M. Newton, "Phylogenetic inference for binary data on dendrograms using Markov chain Monte Carlo," J. Comput. Graph. Stat. vol. 6 pp. 122-131, 1997.
15. N. Metropolis, A. W. Rosenbluth, M. N. Rosenbluth, and A. H. Teller, "Equations of state calculations by fast computing machines," J. Chem. Phys. vol. 21 pp. 1087-1092, 1953.
16. W. J. Murphy, E. Eizirik, S. J. O'Brien, O. Madsen, M. Scally, C. J. Douady, E. Teeling, O. A. Ryder, M. J. Stanhope, W. W. de Jong, and M. S. Springer, "Resolution of the early placental mammal radiation using Bayesian phylogenetics," Science vol. 294 pp. 2348-2351.
17. J. L. Oliver, P. Bernaolo-Galvin, P. Carpena, and R. Roman-Roldan, "Isochore chromosome maps of eukaryotic genomes," Gene vol. 276 pp. 47-56, 2001.
18. R. D. M. Page, "TREEVIEW: An application to display phylogenetic trees on personal computers," Computer Applications in the Biosciences vol. 12 pp. 357-358, 1996.
19. D. B. Phillips and A. F. M. Smith, "Bayesian model comparison via jump diffusions," in W. R. Gilks, S. T. Richardson, and D. J. Spiegelhalter (eds.), Markov Chain Monte Carlo in Practice, Chapman and Hall, 1995.
20. Z. Yang and B. Rannala "Bayesian phylogenetic inference using DNA sequences: a Markov chain Monte Carlo method," Mol. Biol. Evol. vol. 14 pp. 717-724, 1997.