Parallel algorithms for Bayesian phylogenetic inference

Journal of Parallel and Distributed Computing

Volumn 63, Issue 7-8, 2003, Pages 707-718

  Feng, Xizhou ^a   Buell, Duncan A ^a   Rose, John R ^a   Waddell, Peter J ^a  

^a UNIVERSITY OF SOUTH CAROLINA   (United States)

Author keywords

Distributed parallel computation; MCMC; Phylogenetic inference

Indexed keywords

EID: 0142074265     PISSN: 07437315     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0743-7315(03)00079-0     Document Type: Article

References (28)

1. G. Altekar, S. Dwarkadas, J.P Huelsenbeck, F. Ronquist, Parallel Metropolis-coupled Markov chain Monte Carlo for Bayesian phylogenetic inference, Technical Report TR784, Department of Computer Science, University of Rochester, July 2002.
2. C.J. Douady, F. Delsuc, Y. Boucher, W.F. Doolittle, E.J. Douzery, Comparison of Bayesian and maximum likelihood bootstrap measures of phylogenetic reliability, Mol. Biol. Evol. 20 (2003) 248-254.
3. R. Durbin, S. Eddy, G. Mitchison, Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids, 1st Edition, Cambridge University Press, Cambridge, 1997.
4. J. Felsenstein, Evolutionary trees from DNA sequences: a maximum-likelihood approach, J. Mol. Evol. 17 (1981) 368-376.
5. C.J. Geyer, Markov chain Monte Carlo maximum likelihood, in: Computing Science and Statistics: Proceedings of the 23rd Symposium Interface, 1991, pp. 156-163.
6. W.R. Gilks, D.J. Spiegelhalter, S. Richardson, Markov Chain Monto Carlo in Practice, CRC Press, Boca Raton, FL, 1996.
7. P.J. Green, Reversible jump Markov chain Monte Carlo computation and Bayesian model determination, Biometrika 82 (1995) 711-732.
8. W.K. Hastings, Monte Carlo sampling methods using Markov chains and their applications, Biometrika 57 (1970) 97-109.
9. J.P. Huelsenbeck, F. Ronquist, MRBAYES: Bayesian inference of phylogenctic trees, Bioinformatics 17 (2001) 754-755.
10. H. Kishino, M. Hasegawa, Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in Hominoidea, J. Mol. Evol. 29 (1989) 170-179.
11. B. Larget, D. Simon, Markov chain Monte Carlo algorithms for the Bayesian analysis of phylogenetic trees, Mol. Biol. Evol. 16 (1999) 750-759.
12. S. Li, D.K. Pearl, H. Doss, Phylogenetic tree construction using Markov chain Monte Carlo, J. Amer. Statist. Assoc. 95 (2000) 493-508.
13. J.S. Liu, Monte Carlo Strategies in Scientific Computing, Springer Series in Statistics, Harvard University, New York, NY, 2001.
14. J.S. Liu, F. Liang, W.H. Wong, The use of multiple-try method and local optimization in Metropolis sampling, J. Amer. Statist. Assoc. 95 (2000) 121-134.
15. B. Mau, M.A. Newton, B. Larget, Bayesian phylogenetic inference via Markov Chain Monte Carlo methods, Biometrics 55 (1999) 1-12.
16. N. Metropolis, A.W. Rosenbluth, M.N. Rosenbluth, A.H. Teller, E. Teller, Equations of state calculations by fast computing machines, J. Chem. Phys. 21 (1953) 1087-1091.
17. B.M.E. Moret, D.A. Bader, T. Warnow, High-performance algorithm engineering for computational phylogeny, J. Supercomput. 22 (2002) 99-111.
18. R.M. Neal, Probabilistic inference using Markov chain Monte Carlo methods, Technical Report CRG-TR-93-1, Department of Computer Science, University of Toronto, 1993.
19. H.A. Schmidt, K. Strimmer, M. Vingron, A. von Haeseler, TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing, Bioinformatics 18 (2002) 502-504.
20. A.P. Stamatakis, T. Ludwig, H. Meier, M.J. Wolf, Accelerating parallel maximum likelihood-based phylogenetic tree calculations using subtree equality vectors, in: Proceedings of the Supercomputing Conference (SC2002), Baltimore, Maryland, November 2002.
21. C.A. Stewart, D. Hart, D.K. Berry, G.J. Olsen, E.A. Wernert, W. Fischer, Parallel implementation and performance of fastDNAml - a program for maximum likelihood phylogenetic inference, in: Proceedings of the Supercomputing Conference (SC2001), Denver, CO, November 2001.
22. D.L. Swofford, G.J. Olsen, P.J. Waddell, D.M. Hillis, Phylogenetic inference in: D.M. Hillis, C. Moritz, B.K. Mable, (Eds.), Molecular Systematics, 2nd Edition, Sinauer & Associates, Sunderland, MA, 1996, pp. 407-514.
23. P.J. Waddell, Y. Cao, M. Hasegawa, D.P. Mindell, Assessing the Cretaceous superordinal divergence times within birds and placental mammals using whole mitochondrial protein sequences and an extended statistical framework, Systematic Biol. 48 (1999) 119-137.
24. P.J. Waddell, Y. Cao, J. Hauf, M. Hasegawa, Using novel phylogenetic methods to evaluate mammalian mtDNA, including AA invariant sites-LogDet plus site stripping, to detect internal conflicts in the data, with special reference to the position of hedgehog, armadillo, and elephant, Systematic Biol. 48 (1999) 31-53.
25. P.J. Waddell, H. Kishino, R. Ota, A phylogenetic foundation for comparative mammalian genomics, Genome Informatics Ser. 12 (2001) 141-154.
26. P.J. Waddell, H. Kishino, R. Ota, Very fast algorithms for evaluating the stability of ML and Bayesian phylogenetic trees from sequence data, Genome Informatics 13 (2002) 82-92.
27. P.J. Waddell, D. Penny, T. Moore, Extending Hadamard conjugations to model sequence evolution with variable rates across sites, Mol. Phylogene. Evol. 8 (1997) 33-50.
28. Z.H. Yang, B. Rannala, Bayesian phylogenetic inference using DNA sequences: a Markov chain Monte Carlo method, Mol. Biol. Evol. 14 (1997) 717-724.