Search-based optimization

Cladistics

Volumn 19, Issue 4, 2003, Pages 348-355

  Wheeler, Ward C ^a  

^a DIVISION OF INVERTEBRATE ZOOLOGY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CLADISTICS; OPTIMIZATION; PHYLOGENETICS;

EID: 0043241708     PISSN: 07483007     EISSN: None     Source Type: Journal    
DOI: 10.1111/j.1096-0031.2003.tb00378.x     Document Type: Article

References (20)

1. Blanchette, M., Bourque, G., Sankoff, D., 1997. Breakpoint phylogenies. In: Miyano, S., Takugi, T. (Eds.), Genome Informatics. University of Academy Press, Tokyo, pp. 25-34.
2. Blanchette, M., Kunisawa, T., Sankoff, D., 1999. Gene order breakpoint evidence in animal mitochondrial phylogeny. J. Mol. Evol. 49, 193-203.
3. Boore, J.L., Collins, T.M., Stanton, D., Daehler, L.L., Brown, W.M., 1995. Deducing the pattern of arthropod phylogeny from mitochondrial rearrangements. Nature 376, 163-165.
4. Edgecombe, G.D., Giribet, G., Wheeler, W.C., 2002. Phylogeny of Henicopidae (Chilopoda: Lithobiomorpha): a combined analysis of morphology and five molecular loci. Syst. Ent. 27, 31-64.
5. Giribet, G., Edgecombe, G.D., Wheeler, W.C., 2001. Arthropod phylogeny based on eight molecular loci and morphology. Nature 413, 157-161.
6. Gladstein, D.G., 1997. Incremental evaluation and the diagnosis of cladograms. Cladistics 13, 21-26.
7. Goloboff, P.A., 1993. Character optimization and calculation of tree lengths. Cladistics 9, 433-436.
8. Goloboff, P., 1996. PHAST. Program and Documentation, ver. 1.5.
9. Sankoff, D.D., Rousseau, P., 1975. Locating the vertices of a Steiner tree in arbitrary space. Math. Programming 9, 240-246.
10. Sankoff, D., Blanchette, M., 2000. Multiple genome rearrangement and breakpoint. Journal of Computational Biology 5, 555-570.
11. Thompson, J.D., Higgins, D.G., Gibson, T.J., 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22, 4673-4680.
12. Thompson, J.D., Gibson, T.J., Plewniak, F., Jeanmougin, F., Higgins, D.G., 1997. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25, 4876-48821.
13. Wang, L., Jiang, T., 1994. On the complexity of multiple sequence alignment. Journal of Computational Biology 1, 337-348.
14. Wheeler, W.C., 1996. Optimization alignment: the end of multiple sequence alignment in phylogenetics. Cladistics 12, 1-9.
15. Wheeler, W.C., 1998. Alignment characters, dynamic programming, and heuristic solutions. In: DeSalle, R., Schierwater, B. (Eds.), Molecular Approaches to Ecology and Evolution, second ed. Birkhäuser Verlag, Basel, Switzerland, pp. 243-251.
16. Wheeler, W.C., 1999. Fixed character states and the optimization of molecular sequence data. Cladistics 15, 379-385.
17. Wheeler, W.C., 2001. Homology and the optimization of DNA sequence data. Cladistics 17, S3-S11.
18. Wheeler, W.C., Gladstein, D.G., 1994. MALIGN: a multiple sequence alignment program. J. Hered. 85, 417-418.
19. Wheeler, W.C., Gladstein, D.G., 1991-1998. Malign. Program and Documentation. New York, NY. Documentation by Daniel Janies and Ward Wheeler.
20. Wheeler, W.C., Gladstein, D.S., Laet, J.D., 2002. POY, ver. 3.0. Available from 〈ftp.amnh.org/pub/molecular/poy〉 Documentation by Daniel Janies and Ward Wheeler.