Exploring FPGAs for accelerating the phylogenetic likelihood function

IPDPS 2009 - Proceedings of the 2009 IEEE International Parallel and Distributed Processing Symposium

Volumn , Issue , 2009, Pages

  Alachiotis, N ^a,b   Sotiriades, E ^a   Dollas, A ^a   Stamatakis, A ^b  

^a TECHNICAL UNIVERSITY OF CRETE   (Greece)

^b TECHNICAL UNIVERSITY OF MUNICH   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL SEQUENCE DATA; COMPUTATIONAL KERNELS; COMPUTATIONAL SOLUTIONS; DEDICATED COMPUTERS; EVOLUTIONARY HISTORY; EXECUTION TIME; FLOATING POINTS; LIKELIHOOD FUNCTIONS; MOLECULAR DATA; MOORE'S LAW; MULTICORE ARCHITECTURES; MULTIPLE GENES; PARALLEL IMPLEMENTATIONS; PHYLOGENETIC INFERENCE; PHYLOGENETIC TREES; PHYLOGENOMICS; PYROSEQUENCING; SCORING FUNCTIONS; STATISTICAL MODELS;

COMPUTER ARCHITECTURE; DISTRIBUTED PARAMETER NETWORKS; GENES; MAXIMUM LIKELIHOOD;

FIELD PROGRAMMABLE GATE ARRAYS (FPGA);

EID: 70449939435     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/IPDPS.2009.5160929     Document Type: Conference Paper

References (26)

1. M. Margulies, M. Egholm, W.E. Altman, S. Attiya, J.S. Bader, L.A. Bemben, J. Berka, M.S. Braverman, Y.J. Chen, Z. Chen, et al. Genome sequencing in microfabricated high-density picolitre reactors. Nature, 437:376-380, 2005.
2. J. Felsenstein. Evolutionary trees from DNA sequences: a maximum likelihood approach. Journal of Molecular Evolution, 17: 368-376, 1981.
3. B. Chor and T. Tuller. Maximum likelihood of evolutionary trees: hardness and approximation. Bioinformatics, 21(1):97-106, 2005.
4. D.A. Bader, B.M.E. Moret, L. Vawter Industrial applications of high-performance computing for phylogeny reconstruction. Proc. SPIE Commercial Applications for High-Performance Computing, 4528, 159-168, 2001.
5. A. Stamatakis. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics, 22(21):2688-2690, 2006.
6. D. Zwickl. Genetic Algorithm Approaches for the Phylogenetic Analysis of Large Biological Sequence Datasets under the Maximum Likelihood Criterion. PhD thesis, University of Texas at Austin, April 2006.
7. F. Ronquist and J.P. Huelsenbeck. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics, 19(12):1572-1574, 2003.
8. N. Goldman and Z. Yang. Introduction. statistical and computational challenges in molecular phylogenetics and evolution. Philosophical Transactions of The Royal Society B, 363(1512): 3889-3892, 2008.
9. J. Felsenstein. Confidence Limits on Phylogenies: An Approach Using the Bootstrap. Evolution, 39(4):783-791, 1985.
10. M. Ott, J. Zola, S. Aluru, and A. Stamatakis. Large-scale Maximum Likelihood-based Phylogenetic Analysis on the IBM BlueGene/L. On-Line Proceedings of IEEE/ACM Supercomputing Conference 2007, 2007.
11. A. Stamatakis and M. Ott Exploiting Fine-Grained Parallelism in the Phylogenetic Likelihood Function with MPI, Pthreads, and OpenMP: A Performance Study. In Madhu Chetty, Alioune Ngom, and Shandar Ahmad, editors, PRIB, volume 5265 of Lecture Notes in Computer Science, pages 424-435. Springer, 2008.
12. Z. Yang. Maximum likelihood phylogenetic estimation from dna sequences with variable rates over sites. Journal of Molecular Evolution, 39:306-314, 1994.
13. S. Tavare. Some Probabilistic and Statistical Problems in the Analysis of DNA Sequences. Some Mathematical Questions in Biology: DNA Sequence Analysis, 17, 1986.
14. J.D. Bakos. FPGA Acceleration of Gene Rearrangement Analysis. In 15th Annual Symposium on Field- Programmable Custom Computing Machines (FCCM 2007), pages 85-94, 2007.
15. J.D. Bakos, P.E. Elenis, and J. Tang. FPGA Acceleration of Phylogeny Reconstruction for Whole Genome Data. In Proc. of 7th IEEE International Conference on Bioinformatics and Bioengineering (BIBE 2007), pages 888-895, 2007.
16. B.M.E. Moret, J. Tang, L.S. Wang, and T. Warnow. Steps toward accurate reconstructions of phylogenies from geneorder data. J. of Comp. and Sys. Sci., 65(3):508-525, 2002.
17. J.P. Davis, S. Akella, and P.H. Waddell. Accelerating phylogenetics computing on the desktop: experiments with executing UPGMA in programmable logic. In Engineering in Medicine and Biology Society, 2004. IEMBS04. 26th Annual International Conference of the IEEE, volume 2, pages 2864-2868 2004.
18. A.W.F. Edwards and L.L. Cavalli-Sforza. The reconstruction of evolution. Heredity, 18(533):104-105, 1963.
19. L.R. Foulds and R.L. Graham. The Steiner problem in phylogeny is NP-complete. Advances in Applied Mathematics, volume 3, pages 43-49, 1982.
20. P.A. Goloboff, J.S. Farris, and K. Nixon. TNT: Tree Analysis Using New Technology. Program and documentation, version, 1, 2000.
21. T.S.T. Mak and K.P. Lam. Embedded computation of maximum-likelihood phylogeny inference using platform FPGA. In Proceedings of IEEE Computational Systems Bioinformatics Conference (CSB 04), pages 512-514, 2004.
22. T. S.T. Mak and K.P. Lam. FPGA-Based Computation for Maximum Likelihood Phylogenetic Tree Evaluation. In Proceedings of IEEE Computational Systems Bioinformatics Conference (CSB 04),volume 3203 of Lecture Notes in Computer Science, pages 1076-1079, 2004.
23. T.H. Jukes and C.R. Cantor. Evolution of protein molecules. Mammalian Protein Metabolism, 3:21-132, 1969.
24. J. Ripplinger and Jack Sullivan. Does Choice in Model Selection Affect Maximum Likelihood Analysis? Systematic Biology, 57(1):76-85, 2008.
25. G.A. Constantinides. Perturbation analysis for word-length optimization. In 11th Annual IEEE Symposium on Field-Programmable Custom Computing Machines (FCCM 2003), pages 81-90, 2003.
26. A. Stamatakis. Phylogenetic models of rate heterogeneity: A high performance computing perspective. Proceedings of 20th IEEE/ACM International Parallel and Distributed Processing Symposium (IPDPS2006), 2006.