High-Performance Phylogeny Reconstruction Under Maximum Parsimony

Parallel Computing for Bioinformatics and Computational Biology: Models, Enabling Technologies, and Case Studies

Volumn , Issue , 2005, Pages 369-394

  Williams, Tiffani L ^a   Bader, David A ^b   Moret, Bernard M E ^b   Yan, Mi ^c  

^a HARVARD UNIVERSITY   (United States)

^b UNIVERSITY OF NEW MEXICO   (United States)

^c TEXAS A AND M UNIVERSITY   (United States)

Author keywords

High performance phylogeny reconstruction under MP; Maximum parsimony (MP); Sequence alignment on "true" evolutionary tree

Indexed keywords

EID: 78649720352     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1002/0471756504.ch16     Document Type: Chapter

References (43)

1. D. Bader, B. M. Moret, and L. Vawter, Industrial Applications of High-Performance Computing for Phylogeny Reconstruction, in H. Siegel, Ed., Proceedings of the SPIE Commercial Applications for High-performance Computing, Vol. 4528, Denver, CO. SPIE, 2001, pp. 159-168.
2. J. Cracraft, The seven great questions of systematic biology: an essential foundation for conservation and the sustainable use of biodiversity, Ann. Missouri Bot. Gard., 89, 127-144 (2002).
3. D. L. Swofford, PAUP*: Phylogenetic Analysis Using Parsimony (and other Methods). Sinauer Associates, Sunderland, Massachusetts, Version 4.0.
4. J. Felsenstein, Phylogenetic inference package (PHYLIP), version 3.2, Cladistics, 5, 164-166 (1989).
5. J. P. Huelsenbeck and F. Ronquist, "MR-BAYES: Bayesian inference of phylogenetic trees, " Bioinformatics, 17 (8), 754-755 (2001).
6. P. Goloboff, Analyzing large data sets in reasonable times: solutions for composite optima, Cladistics, 15, 415-428 (1999).
7. B. Moret, J. Tang, and T. Warnow, Reconstructing Phylogenies from Gene-Content and Gene-Order Data, in O. Gascuel, Ed., Mathematics of Evolution and Phylogeny, Oxford University Press, 2005, pp. 321-352.
8. B. M. E. Moret and T. Warnow, "Advances in Phylogeny Reconstruction from Gene Order and Content Data, " in Molecular Evolution: Producing the Biochemical Data, Part B, E. A. Zimmer and E. H. Roalson, eds., Vol. 395 of Methods in Enzymology, Elsevier (2005), 673-700.
9. T. Jukes, Evolution of Protein Molecules, in M. Munro, Ed., Mammalian Protein Metabolism, Vol. III, Academic Press, New York, 1969, pp. 21-132.
10. M. Kimura, A simple model for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences, J. Mol. Evol., 16, 111-120 (1980).
11. N. Saitou and M. Nei, The neighbor-joining method: A new method for reconstructing phylogenetic trees, Mol. Biol. Evol., 4, 406-425 (1987).
12. O. Gascuel, BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data, Mol. Biol. Evol., 14, 685-695 (1997).
13. W. Bruno, N. Socci, and A. Halpern, Weighted neighbor joining: a likelihood-based approach to distance-based phylogeny reconstruction, Mol. Biol. Evol., 17 (1), 189-197 (2000).
14. L. R. Foulds and R. L. Graham, The Steiner problem in phylogeny is NP-complete, Adv. App. Math., 3, 43-49 (1982).
15. M. Steel, The maximum likelihood point for a phylogenetic tree is not unique, Systematic Biol., 43 (4), 560-564 (1994).
16. W. M. Fitch, Toward defining the course of evolution: minimal change for a specific tree topology, Syst. Zool., 20, 406-416 (1971).
17. G. Olsen, H. Matsuda, R. Hagstrom, and R. Overbeek, fastdnaml: a tool for construction of phylogenetic trees of DNA sequences using maximum likelihood, Comput. Appl. Biosci., 10, 41-48 (1994).
18. S. Guindon and O. Gascuel, A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood, Syst. Biol., 52 (5), 696-704 (2003).
19. M. Sanderson, B. Baldwin, G. Bharathan, C. Campbell, D. Ferguson, J. Porter, C. V. Dohlen, M. Wojciechowski, and M. Donoghue, The growth of phylogenetic information and the need for a phylogenetic database, Systematic Biology, 42, 562-568 (1993).
20. B. Moret, U. Roshan, and T. Warnow, Sequence Length Requirements for Phylogenetic Methods, in Proceedings of the second International Workshop Algorithms in Bioinfor-matics (WABI'02), Vol. 2452, Lecture Notes in Computer Science, Springer-Verlag, 2002, pp. 343-356.
21. L. Nakhleh, B. Moret, U. Roshan, K. S. John, J. Sun, and T. Warnow, The Accuracy of Fast Phylogenetic Methods for Large Data Sets, in Proceedings of the seventh Pacific Symposium Biocomputing (PSB'2002), World Scientific Publication, 2002, pp. 211-222.
22. L. Nakhleh, U. Roshan, K. St. John, J. Sun, and T. Warnow, Designing Fast Converging Phylogenetic Methods, in Proceedings of the Ninth International Conference on Intelligent Systems for Molecular Biology (ISMB'01), Vol. 17, Bioinformatics, Oxford Univeristy Press, 2001, pp. S190-S198.
23. W. Fitch, On the problem of discovering the most parsimonious tree, Am. Nat. 111 (978), 223-257 (1977).
24. M. Hendy and D. Penny, Branch and bound algorithms to determine minimal evolutionary trees, Math. Biosci., 59, 277-290 (1982).
25. D. A. Bader, W. E. Hart, and C. A. Phillips, Parallel Algorithm Design for Branch and Bound, in H. Greenberg, Ed., Tutorials on Methodologies and Applications in Operation Research, Chapter 5, Academic Press, 2004, pp. 1-44.
26. M. Yan and D. A. Bader, High-Performance Algorithms for Phylogeny Reconstruction with Maximum Parsimony, in S. Aluru, Ed., Handbook on Computational Molecular Biology, Chapman & Hall/CRC Computer and Information Science Series, 2005, in press.
27. P. J. Purdom, P. Bradford, K. Tamura, and S. Kumar, Single column discrepancy and dynamic max-mini optimization for quickly finding the most parsimonious evolutionary trees, Bioinfomatics, 2 (16), 140-151 (2000).
28. D. Knuth, The Art of Computer Programming: Sorting and Searching, Vol. 3, Addison-Wesley, Reading, MA, 1973.
29. P. A. Goloboff, Character optimization and calculation of tree lengths, Cladistics, 9, 433436 (1993).
30. D. S. Gladstein, Efficient incremental character optimization, Cladistics, 13, 21-26 (1997).
31. D. Huson, S. Nettles, and T. Warnow, Disk-covering, a fast-converging method for phylogenetic tree reconstruction, J. Comput. Biol., 6, 369-386 (1999).
32. D. Huson, L. Vawter, and T. Warnow, Solving Large-scale Phylogenetic Problems using DCM2, in Proceedings of the 7th International Conference on Intelligent Systems for Molecular Biology (ISMB'99), AAAI Press, 1999, pp. 118-129.
33. U. Roshan, B. M. E. Moret, T. L. Williams, and T. Warnow, Rec-I-DCM3: A Fast Algorithmic Technique for Reconstructing Large Phylogenetic Trees, in Proceedings of the IEEE Computer Society Bioinformatics Conference (CSB 2004), IEEE Press. 2004, pp. 98-109.
34. T. Warnow, B. Moret, and K. St. John, Absolute Convergence: True Trees from Short Sequences, in Proceedings of the 12th Ann. ACM-SIAM Symp. Discrete Algorithms (S0DA'01), SIAM Press, 2001, pp. 186-195.
35. J. Tang and B. Moret, Scaling Up Accurate Phylogenetic Reconstruction from Gene Order Data, in Proceedings of the 11th International Conference on Intelligent Systems for Molecular Biology (ISMB'03), Vol. 19 (Suppl. 1), Bioinformatics, 2003, pp. 1305-1312.
36. O. Bininda-Emonds, Ratchet Implementation in PAUP*4.0b10. http://www.tierzucht.tum.de:8080/WWW/Homepages/Bininda-Emonds.
37. B. Moret, Towards a Discipline of Experimental Algorithmics, in M. Goldwasser, D. Johnson, and C. McGeoch, Eds., Data Structures, Near Neighbor Searches, and Methodology: Fifth and Sixth DIMACS Implementation Challenges, Vol. 59, DIMACS Monographs, American Mathematical Society, 2002.
38. B. Moret and T. Warnow, Reconstructing Optimal Phylogenetic Trees: A Challenge in Experimental Algorithmics, in R. Fleischer, B. Moret, and E. Schmidt, Eds., Experimental Algorithmics, Vol. 2547, Lecture Notes in Computer Science, Springer-Verlag, 2002, pp. 163-180.
39. T. Williams, B. M. Berger-Wolf, U. Roshan, and T. Warnow, The Relationship Between Maximum Parsimony Scores and Phylogenetic Tree Topologies, Technical Report TR-CS-2004-04, Department of Computer Science, The University of New Mexico, 2004.
40. J. Wuyts, Y. V. de Peer, T. Winkelmans, and R. D. Wachter, The European database on small subunit ribosomal RNA, Nucl. Acids Res., 30, 183-185 (2002).
41. M. Kallerjo, J. S. Farris, M. W. Chase, B. Bremer, and M. F. Fay, Simultaneous parsimony jackknife analysis of 2538 rbcL DNA sequences reveals support for major clades of green plants, land plants, seed plants, and flowering plants, Plant. Syst. Evol., 213, 259-287 (1998).
42. B. Maidak, J. Cole, T. Lilburn, C. T. Parker, Jr., P. R. Saxman, J. Stredwick, G. Garrity, B. Li, G. Olsen, S. P. Pamanik, T. Schmidt, and J. Tiedje, The RDP (ribosomal database project) continues, Nucl. Acids Res., 28, 173-174 (2000).
43. J. Felsenstein, Inferring Phylogenies, Sinauer Associates, 2003.