Analyzing large data sets in reasonable times: Solutions for composite optima

Cladistics

Volumn 15, Issue 4, 1999, Pages 415-428

  Goloboff, Pablo A ^a  

^a Instituto Miguel Lillo ^*  (Argentina)

Author keywords

[No Author keywords available]

Indexed keywords

CLADISTICS;

EID: 0033499153     PISSN: 07483007     EISSN: None     Source Type: Journal    
DOI: 10.1006/clad.1999.0122     Document Type: Article

References (21)

1. Chase M. W., Soltis D. E., Olmstead R. G., Morgan D., Les D. H., Mishler B. D., Duvall M. R., Price R. A., Hills H. G., Qiu Y.-L., Kron K. A., Rettig J. H., Conti E., Palmer J. D., Manhart J. R., Sytsma K. J., Michaels H. J., Kress W. J., Karol K. G., Clark W. D., Hedren M., Gaut B. S., Jansen R. K., Kim K.-J., Wimpee C. F., Smith J. F., Furnier G. R., Strauss S. H., Xiang Q.-Y., Plunkett G. M., Soltis P. S., Swensen S. M., Willimas S. E., Gadek P. A., Quinn C. J., Eguiarte L. E., Golenberg E., Learn G. H. Jr., Graham S. W., Barret S.C. H., Dayanandan S., Albert V. A. Phylogenetics of seed plants: An analysis of nucleotide sequences from the plastid gene rbcL. Ann. Mol. Bot. Gard. 80:1993;528-580.
2. Coddington J., Scharff N. Problems with zero-length branches. Cladistics. 10:1994;415-423.
3. Farris J., Albert V., Källersjö M., Lipscomb D., Kluge A. Parsimony jackknifing outperforms neighbor-joining. Cladistics. 12:1996;99-124.
4. Felsenstein J. PHYLIP: Phylogeny Inference Package. 1993;University of Washington, Seattle.
5. Giribet, G, and, Wheeler, W. The position of the arthropods in the animal kingdom: Ecdisozoa, islands, and the parsimony ratchet, Mol. Phylogenet. Evol, in press.
6. Gladstein D. Efficient incremental character optimization. Cladistics. 13:1997;21-26.
7. Goloboff P. NONA: A Tree Searching Program. Program and documentation. 1994.
8. Goloboff P. Methods for faster parsimony analysis. Cladistics. 12:1996;199-220.
9. Kirkpatrick S., Gellat C., Vecchi M. Optimization by simulated annealing. Science. 220:1983;671-680.
10. Liebherr J. K., Zimmerman E. C. Cladistic analysis, phylogeny, and biogeography of the Hawaiian Platynini (Coleoptera: Carabidae). Syst. Entomol. 23:1998;101-136.
11. Lipscomb D., Farris J., Kallersjo M., Tehler A. Support, ribosomal sequences and the phylogeny of the eukaryotes. Cladistics. 14:1998;303-338.
12. Maddison D. The discovery and importance of multiple islands of most parsimonious trees. Syst. Zool. 40:1991;315-328.
13. Moilanen A. Searching for most parsimonious trees with simulated evolutionary optimization. Cladistics. 15:1999;39-50.
14. Nixon K. C. The parsimony ratchet a new method for rapid parsimony analysis. Cladistics. 15:1999;407-414.
15. Platnick N. An empirical comparison of microcomputer parsimony programs. Cladistics. 3:1987;121-144.
16. Rice K., Donoghue M., Olmstead R. Analyzing large data sets: rbcL 500 revisited. Syst. Biol. 46:1997;554-563.
17. Ronquist F. Fast Fitch-parsimony algorithms for large data sets. Cladistics. 14:1998;387-400.
18. Soltis D., Soltis P., Mort M., Chase M., Savolainen V., Hoot S., Morton C. Inferring complex phylogenies using parsimony: An empirical approach using three large DNA data sets for angiosperms. Syst. Biol. 47:1998;32-42.
19. Swofford D. PAUP: Phylogenetic Analysis Using Parsimony, version 3.1. Program and documentation. 1993;Laboratory of Molecular Systematics, Smithsonian Institution, Washington.
20. Swofford D. PAUP*: Phylogenetic Analysis Using Parsimony (* and Other Methods), version 4. 1998;Sinauer Associates, Sunder land.
21. Swofford D., Olsen G., Waddell P., Hillis D. Phylogenetic inference. Hillis D., Moritz C., Mable B. "Molecular Systematics" 1996;407-514 Sinauer Associates, Sunderland.