Phylogenetic Parameter Estimation on COWs - Parallel Computing for Bioinformatics and Computational Biology - page 367

REFERENCES
1. J. Felsenstein, The number of evolutionary trees, Syst. Zool. , 27, 27-33 (1978).
2. H. Bodlaender, M. Fellows, and T. Warnow, Two Strikes Against Perfect Phylogeny, in
Proceedings of the 19th International Colloquium on Automata, Language, and Program-
ming (ICALP 1992) , Vol. 623 of Lecture Notes in Computer Science , Springer, NewYork,
1992, pp. 273-283.
3. W. H. E. Day and D. Sankoff, Computational complexity of inferring phylogenies by
compatibility, Syst. Zool. , 35, 224-229 (1986).
4. L. R. Foulds and R. L. Graham, The Steiner problem in phylogeny is NP-complete,
Adv. Appl. Math. , 3, 43-49 (1982).
4a. B. Chor and T. Tuller, Maximum Likelihood of Evolutionary Trees is Hard, Proceedings of
the 9thAnnual International conference on Research in Computational Molecular Biology
(RECOMB 2005), Vol. 3500 of Lecture Notes in Computer Science, Springer, Berlin,
2005, pp. 296-310.
5. A. D. Baxevanis, D. B. Davison, R. D. M. Page, G. Stormo, and L. Stein, Eds., Current
Protocols in Bioinformatics , Wiley and Sons, NewYork, USA, 2002.
6. J. Felsenstein, Infering Phylogenies , SinauerAssociates, Sunderland, Massachusetts, 2004.
7. D. L. Swofford, G. J. Olsen, P. J. Waddell, and D. M. Hillis, Phylogeny Reconstruction, in
D. M. Hillis, C. Moritz, and B. K. Mable, Eds., Molecular Systematics , SinauerAssociates,
Sunderland, Massachusetts, 2nd ed., 1996, pp. 407-514.
8. J. Felsenstein, Evolutionary trees from DNA sequences: A maximum likelihood approach,
J. Mol. Evol. , 17, 368-376 (1981).
9. G. J. Olsen, H. Matsuda, R. Hagstrom, and R. Overbeek, fastDNAml: A tool for construc-
tion of phylogenetic trees of DNA sequences using maximum likelihood, Comput. Appl.
Biosci. , 10, 41-48 (1994).
10. O. Trelles, On the parallelisation of bioinformatics applications, Brief. Bioinform. ,2,
181-194 (2001).
11. G. M. Amdahl, Validity of the Single Processor Approach to Achieving Large Scale
Computing Capabilities, in American Federation of Information Processing Societies Con-
ference Proceedings: Spring Joint Computing Conference (AFIPS 1967) , Vol. 30, Afips
Press, Reston, Va, 1967, pp. 483-485.
12. H. A. Schmidt, K. Strimmer, M. Vingron, and A. von Haeseler, TREE-PUZZLE:
Maximum likelihood phylogenetic analysis using quartets and parallel computing,
Bioinformatics , 18, 502-504 (2002).
13. K. Strimmer and A. von Haeseler, Quartet puzzling: A quartet maximum-likelihood
method for reconstructing tree topologies, Mol. Biol. Evol. , 13, 964-969 (1996).
14. J. Sullivan, K. E. Holsinger, and C. Simon, The effect of topology on estimates of among-
site rate variation. J. Mol. Evol. , 42, 308-312 (1996).
15. Z. Yang, Maximum-likelihood models for combined analyses of multiple sequence data,
J. Mol. Evol. , 42, 587-596 (1996).
16. W. Gropp, S. Huss-Lederman,A. Lumsdaine, E. Lusk, B. Nitzberg,W. Saphir, andM. Snir,
MPI: The Complete Reference. The MPI Extensions , 2nd ed., Vol. 2, The MIT Press,
Cambridge, Massachusetts, 1998.
17. M. Snir, S.W. Otto, S. Huss-Lederman, D.W.Walker, and J. Dongarra, MPI: The Complete
Reference — The MPI Core , Vol. 1, 2nd ed., The MIT Press, Cambridge, Massachusetts,
1998.