Parallel implementation and performance of fastDNAml - a program for maximum likelihood phylogenetic inference

Proceedings of the International Conference on Supercomputing

Volumn , Issue , 2001, Pages 20-

  Stewart, Craig A ^a   Hart, David ^a   Berry, Donald K ^a   Olsen, Gary J ^b   Wernert, Eric A ^a   Fischer, William ^a  

^a INDIANA UNIVERSITY   (United States)

^b UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

Author keywords

bioinformatics; maximum likelihood; parallel applications; phylogenetics; scalability

Indexed keywords

APPLICATION PROGRAMS; COMPUTER OPERATING SYSTEMS; MAXIMUM LIKELIHOOD ESTIMATION; MESSAGE PASSING; TREES (MATHEMATICS);

DNA DATA; DNA SEQUENCE DATA; MA XIMUM LIKELIHOODS; MAXIMUM-LIKELIHOOD; PARALLEL APPLICATION; PARALLEL IMPLEMENTATIONS; PARALLEL PERFORMANCE; PHYLOGENETIC INFERENCE; PHYLOGENETIC TREES; PHYLOGENETICS;

PHYLOGENETIC;

EID: 85129670957     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1145/582034.582054     Document Type: Conference Paper

References (28)

1. Joint Center for Structural Genomics. Home page, http://www. jcsg. org/, accessed May 2001.
2. Korber, B., M. Muldoon, J. Theiler, F. Gao, R. Gupta, A. Lapedes, B. H. Hahn, S. Wolinsky, T. Bhattacharya. 2000. Timing the Ancestor of the HIV-1 Pandemic Strains, http://www. sciencemag. org/cgi/content/full/288/5472/1789, accessed May 2001.
3. Olsen, G. J., H. Matsuda, R. Hagstrom, and R. Overbeek. 1994. fastDNAml: A tool for construction of phylogenetic trees of DNA sequences using maximum likelihood. Comput. Appl. Biosci. 10: 41-48.
4. Olsen, G. J. Home page. http://geta. life. uiuc. edu/~gary/, accessed May 2001.
5. Felsenstein, J. 1981. Evolutionary trees from DNA sequences: A maximum likelihood approach. J. Mol. Evol. 17: 368-376.
6. Stewart, C. A., T. W. Tan, M. Buckhorn, D. Hart, D. K. Berry, L. Zhang, E. Wernert, M. Sakharkar, W. Fischer, D. F. McMullen. 2000. Evolutionary biology and high performance computing. In: R. F. Enenkel. Software Tools for Computational Biology, http://www. cas. ibm. com/archives/1999/workshop_report/bio. html, accessed May 2001.
7. Felsenstein, J. 1978. The number of evolutionary trees. Syst. Zool. 27: 27-33.
8. National center for biotechnology information. Home page, http://www. ncbi. nlm. nih. gov/, accessed May 2001.
9. Maidak B. L., J. R. Cole, T. G. Lilburn, C. T. Parker Jr., P. R. Saxman, R. J. Farris, G. M. Garrity, G. J. Olsen, T. M. Schmidt, J. M. Tiedje. 2001. The RDP-II (Ribosomal Database Project). Nucleic Acids Res. 29 (1): 173-4
10. Maddison, D. R. and W. P. Maddison. 1998. The Tree of Life: A multi-authored, distributed Internet project containing information about phylogeny and biodiversity. http://phylogeny. arizona. edu/tree/phylogeny. html, accessed July 2001.
11. Bodlaender, H., M. Fellows, and T. Warnow. 1992. Two strikes against perfect phylogeny. pp. 273-283 In: Proceedings of the 19th International Colloquium on Automata, Languages, and Programming, Lecture Notes in Computer Science, Springer-Verlag, NY.
12. Hershkovitz, M. A., and D. D. Leipe. 1998. Phylogenetic analysis. In: Bioinformatics: A practical guide to the analysis of genes and proteins. A. D. Baxevanis and B. F. F. Ouelette (Eds.), pp. 189-230. New York: Wiley-Liss.
13. Jermiin, L. S., G. J. Olsen, and S. Easteal. 1997. Majority rule consensus of maximum likelihood trees. Mol. Biol. Evol. 14: 1296-1302.
14. Swofford, D. L., G. J. Olsen, P. J. Waddell, and D. M. Hillis. 1996. Phylogenetic inference. In: Molecular Systematics, 2nd edition D. M. Hillis, C. Moritz and B. K. Mable (Eds.), pp. 407-514 Sunderland, MA: Sinauer Associates.
15. Sarin, V., A. Grama, and A. Sameh. 1998. Analyzing the Error Bounds of Multipole-Based Treecodes. Proceedings of the IEEE/ACM SC98 Conference. Orlando, FL, Nov 1998.
16. Van de Peer, Y., P. De Rijk, J. Wuyts, T. Winkelmans, and R. De Wachter. 2000. The European small subunit ribosomal RNA database. Nucleic Acids Research 28 (1): 175-6.
17. Papakhian, M. The UITS Research SP system, http://spwww. iu. edu/, accessed May 2001.
18. Snell, Q., M. Whiting, M. Clement, and D. McLaughlin. 2000. Parallel phylogenetic inference. Proceedings of the IEEE/ACM SC2000 Conference. Dallas, TX, Nov 2000.
19. Bader, D. A., B. M. E. Moret, T. Warnow, S. K. Wyman, and M. Yan. 2001. High-performance algorithm engineering for gene-order phylogenies. DIMACS Workshop on Whole Genome Comparison, Rutgers University. http://www. cs. utexas. edu/users/stacia/papers/dimacs. pdf, accessed May 2001.
20. Blanchette, M., G. Bourque, and D. Sankoff. 1997. Breakpoint phylogenies. Genome Informatics 1997 (Eds: S. Miyano and T. Takagi) Universal Academy Press, Tokyo, pp. 5-34.
21. Roshan, U., L. Nakhleh, J. Sun, and T. Warnow. 2001. Designing fast converging methods in phylogenetics: An experimental study. Proceedings of Intelligent Systems for Molecular Biology (ISMB) 2001, Copenhagen. http://bioinformatics. oupjournals. org/content/vol17/suppl_1/, accessed July 2001.
22. Ceron, C., J. Dopazo, E. L. Zapata, J. M. Carazo, and O. Trelles. 1998. Parallel implementation of DNAml program on message-passing architectures. Parallel Computing 24: 701-716.
23. Wernert, E. TreeViewer for maximum likelihood analysis of phylogenetic data, http://www. avl. iu. edu/projects/DNAml/, accessed May 2001.
24. Open Inventor. http://www. sgi. com/software/inventor/, accessed July 2001.
25. Hart, D. Maximum Likelihood Analysis of Phylogenetic Data, http://www. indiana. edu/~rac/hpc/fastDNAml/index. html, accessed May 2001.
26. Hein, J. 1989. A tree reconstruction method that is economical in the number of pairwise comparisons used. Mol. Biol. Evol. 6: 669-684.
27. Olsen, G. J. 1988. Phylogenetic analysis using ribosomal RNA. Methods Enzymol. 164: 793-812.
28. Livny, M. The Condor Project Homepage. http://www. cs. wisc. edu/condor/, accessed July 2001.