New approaches for reconstructing phytogenies from gene order data

Bioinformatics

Volumn 17, Issue SUPPL. 1, 2001, Pages

  Moret, Bernard M E ^a   Wang, Li San ^a   Warnow, Tandy ^a   Wyman, Stacia K ^a  

^a NONE

Author keywords

[No Author keywords available]

Indexed keywords

ANGIOSPERM; ARTICLE; BIOLOGICAL MODEL; BIOLOGY; CHLOROPLAST; EVOLUTION; GENETIC DATABASE; GENETIC PROCEDURES; GENETICS; GENOME; PHYLOGENY; STATISTICS;

ANGIOSPERMS; CHLOROPLASTS; COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; EVOLUTION; GENETIC TECHNIQUES; GENOME, PLANT; MODELS, GENETIC; PHYLOGENY;

EID: 0035229986     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/17.suppl_1.S165     Document Type: Article

References (26)

1. Atteson, K. (1999). The performance of the neighbor-joining methods of phylogenetic reconstruction. Algorithmica 25(2/3), 251-278.
2. Bader, D., A. Illendula, and B. Moret (2001). Using PRAM algorithms on a uniform-memory-access shared-memory architecture. Report 2001-03, Dept. of Comput. Sci., U. New Mexico.
3. Bader, D. and B. Moret (2000). GRAPPA runs in record time. HPC Wire 9(47).
4. Bader, D., B. Moret, and M. Yan (2000). A fast linear-time algorithm for inversion distance with an experimental comparison. Report 2000-42, Dept. of Comput. Sci., U. New Mexico.
5. Blanchette, M., G. Bourque, and D. Sankoff (1997). Breakpoint phylogenies. In S. Miyano and T. Takagi (Eds.), Genome Informatics 1997, pp. 25-34. Tokyo: Univ. Academy Press.
6. Caprara, A. (1999). Formulations and hardness of multiple sorting by reversals. In Proc. 3rd Int'l Conf. on Comput. Mol. Biol. RECOMB99, pp. 84-93. ACM Press.
7. Conover, W. (1999). Practical Nonparametric Statistics, 3rd ed. John Wiley & Sons.
8. Cosner, M., R. Jansen, B. Moret, L. Raubeson, L. Wang, T. Warnow, and S. Wyman (2000a). An empirical comparison of phylogenetic methods on chloroplast gene order data in Campanulaceae. In D. Sankoff and J. Nadeau (Eds.), Comparative Genomics, pp. 99-122. Kluwer Acad. Pubs.
9. Cosner, M., R. Jansen, B. Moret, L. Raubeson, L. Wang, T. Warnow, and S. Wyman (2000b). A new fast heuristic for computing the breakpoint phylogeny and experimental phylogenetic analyses of real and synthetic data. In Proc. 8th Int'l Conf. on Intelligent Systems for Mol. Biol. ISMB-2000, pp. 104-115.
10. Downie, S. and J. Palmer (1992). Use of chloroplast DNA rearrangements in reconstructing plant phylogeny. In P. Soltis, D. Soltis, and J. Doyle (Eds.), Plant Molecular Systematics, pp. 14-35. Chapman and Hall.
11. Held, M. and R. Karp (1970). The travelling salesman problem and minimum spanning trees. Oper. Res. 18, 1138-1162.
12. Huson, D., S. Nettles, K. Rice, T. Warnow, and S. Yooseph (1999a). Hybrid tree reconstruction methods. ACM J. Experimental Algorithmics 4(5). www.jea.acm.org/1999/HusonHybrid/.
13. Huson, D., K. Smith, and T. Warnow (1999b). Correcting large distances for phylogenetic reconstruction. In Proc. 3rd Workshop on Algorithm Engineering WAE99, pp. 273-286. Springer Verlag. LNCS 1668.
14. Johnson, D. and L. McGeoch (1997). The traveling salesman problem: a case study. In E. Aarts and J. Lenstra (Eds.), Local Search in Combinatorial Optimization, pp. 215-310. John Wiley.
15. Meidanis, J., M. Walter, and Z. Dias (2000). Reversal distance of signed circular chromosomes, unpublished.
16. Moret, B. (2001). Towards a discipline of experimental algorithmics. In D. Johnson and C. McGeoch (Eds.), DIMACS Monographs in Disc. Math, and Theor. Comput. Sci. to appear.
17. Moret, B., D. Bader, and T. Warnow (2001a). High-performance algorithm engineering for computational phylogenetics. In Proc. 2001 Int'l Conf. Computational Sci. ICCS 2001. Springer Verlag, to appear.
18. Moret, B., S. Wyman, D. Bader, T. Warnow, and M. Yan (2001b). A new implementation and detailed study of breakpoint analysis. In Proc. 6th Pacific Symp. Biocomputing PSB 2001, pp. 583-594. World Scientific Pub.
19. Nadeau, J. and B. Taylor (1984). Lengths of chromosome segments conserved since divergence of man and mouse. Proc. Nat'l Acad. Sci. USA 81, 814-818.
20. Olmstead, R. and J. Palmer (1994). Chloroplast DNA systematics: a review of methods and data analysis. Amer. J. Bot. 81, 1205-1224.
21. Palmer, J. (1992). Chloroplast and mitochondrial genome evolution in land plants. In R. Herrmann (Ed.), Cell Organelles, pp. 99-133. Springer Verlag.
22. Pe'er, I. and R. Shamir (1998). The median problems for break-points are NP-complete. Elec. Colloq. on Comput. Complexity 71.
23. Raubeson, L. and R. Jansen (1992). Chloroplast DNA evidence on the ancient evolutionary split in vascular land plants. Science 255, 1697-1699.
24. Sankoff, D. and M. Blanchette (1998). Multiple genome rearrangement and breakpoint phylogeny. J. Comp. Biol. 5, 555-570.
25. Swofford, D., G. Olson, P. Waddell, and D. Hillis (1996). Phylogenetic inference. In D. Hillis, C. Moritz, and B. Mable (Eds.), Molecular Systematics, 2nd ed., Chapter 11. Sinauer Associates.
26. Wang, L. and T. Warnow (2001). Estimating true evolutionary distances between genomes. In Proc. 33rd Symp. on Theory of Comp. STOC01. ACM Press, to appear.