Jumpstarting phylogenetic analysis

International Journal of Bioinformatics Research and Applications

Volumn 2, Issue 1, 2006, Pages 19-35

  Mecham, Jesse ^a   Clement, Mark ^a   Snell, Quinn ^a   Freestone, Todd ^a   Seppi, Kevin ^a   Crandall, Keith ^b,c  

^a 3361 TMCB   (United States)

^b BRIGHAM YOUNG UNIVERSITY   (United States)

^c NONE   (United States)

Author keywords

Alignment; Jumpstart; Phylogenetics

Indexed keywords

ALGORITHM; CONFERENCE PAPER; DNA ISOLATION; DNA SEQUENCE; GENOMICS; HUMAN IMMUNODEFICIENCY VIRUS; NONHUMAN; PHYLOGENY;

HUMAN IMMUNODEFICIENCY VIRUS;

EID: 33646449853     PISSN: 17445458     EISSN: 17445493     Source Type: Journal    
DOI: 10.1504/IJBRA.2006.009191     Document Type: Conference Paper

References (36)

1. Clark, A., Weiss, K., Nickerson, D., Taylor, S., Buchanan, A., Stengard, J., Salomaa, V., Vartiainen, E., Perola, M., Boerwinkle, E. and Sing, C. (1998) 'Haplotype structure and population genetic inferences from nucleotide-sequence variation in human lipoprotein lipase', American Journal of Human Genetics, Vol. 63, pp.595-612.
2. Crandall, K. (1996) 'Multiple interspecies transmissions of human and simian T-cell leukemia/lymphoma virus type I sequences', Molecular Biology and Evolution, Vol. 13, pp.115-131.
3. Crandall, K.A. and Buhay, J.E. (2004) 'Genomic databases and the tree of life', Science, Vol. 306, pp.1144-1145.
4. DeSalle, R. (1995) 'Molecular approaches to biogeographic analysis of Hawaiian Drosophilidae', in Wagner, W.L. and Funk, V.A. (Eds.): Hawaiian Biogeography, Smithsonian Institute Press, Washington DC, pp.72-89.
5. Enserink, M. (1999) 'Groups race to sequence and identify New York virus', Science, Vol. 286, pp.206-207.
6. Felsenstein, J. (1978) 'The number of evolutionary trees', Systematic Zoology, Vol. 27, pp.27-33.
7. Felsenstein, J. (2002) PHYLIP, version 3.6, Department of Genome Sciences, University of Washington, http://evolution.genetics.washington.edu/ phylip.html.
8. Felsenstein, J. (2004) Inferring Phylogenies, Sinauer Associates, Sunderland, MA.
9. Goloboff, P. (1997) NONA, Available via FTP with registration from Willi Hennig Society, http://www.cladistics.com/about_nona.htm.
10. Hillis, D., Miritz, C. and Mable, B. (1996) Molecular Systematics, Sinauer Assc., Sunderland.
11. Lanciotti, R.S., Roehrig, J.T., Deubel, V., Smith, J., Parker, M., Steele, K., Crise, B., Volpe, K.E., Crabtree, M.B., Scherret, J.H., Hall, R.A., MacKenzie, J.S., Cropp, C.B., Panigrahy, B., Ostlund, E., Schmitt, B., Malkinson, M., Banet, C., Weissman, J., Komar, N., Savage, H.M., Stone, W., McNamara, T. and Gubler, D.J. (1999) Origin of the West Nile virus responsible for an outbreak of encephalitis in the Northeastern United States', Science, Vol. 286, pp.2333-2337.
12. Nixon, K. (1998) 'The parsimony ratchet: a new method for rapid parsimony analysis and broad sampling of tree islands in large data sets', Program of the 17th Meeting of the Willi Hennig Society, Sao Paulo, Brazil, p.59.
13. Pagel, M. (1999) 'Inferring the historical patterns of biological evolution', Nature, Vol. 401, pp.877-884.
14. Quinn, S., Whiting, M., Clement, M. and McLaughlin, D. (2000) 'Parallel phylogenetic inference', Proceedings of Supercomputing, Dallas, Texas, Article No. 35, ISBN: 0-7803-9802-5.
15. Swofford, D. (1993) PAUP: Phylogenetic Analysis Using Parsimony, Smithsonian Institution, Washington DC, http://paup.csit.fsu.edu.
16. Templeton, A.R., Maxwell, T., Posada, D., Stengard, J.H., Boerwinkle, E. and Sing, C.F. (2005) 'Tree scanning: a method for using haplotype trees in phenotype/genotype association studies', Genetics, Vol. 169, pp.441-453.
17. Achard, F., Vaysseix, G. and Barillot, E. (2001) 'XML, bioinformatics and data integration', Bioinformatics, Vol. 17, No. 2, pp.115-125.
18. Bhandarkar, M., Budescu, G., Humphrey, W., Izaguirre, J., Izrailev, S., Kale, L., Kosztin, D., Molnar, F., Phillips, J. and Schulten, K. (1999) 'BioCoRE: a collaboratory for structural biology', Proceedings of the SCS International Conference on Web-Based Modeling and Simulation, San Francisco, California, pp.242-251.
19. BugZilla (2003) http://bugzilla.mozilla.org/.
20. Foster, I. and Kesselman, C. (1997) 'Globus: a metacomputing infrastructure toolkit', International Journal of Supercomputer Applications, Vol. 11, No. 2, pp.115-128.
21. Foster, I., Kesselman, C., Nick, J. and Tuecke, S. (2002) 'The physiology of the grid: an open grid services architecture for distributed systems integration', Open Grid Service Infrastructure Working Group, Global Grid Forum.
22. GenBank (2005) National Center for Biotechnology Information, http://www.ncbi.nlm.nih.gov/Genbank.
23. Gnutella (2003) http://www.gnutella.com.
24. Grimshaw, A. and Wulf, W. (1997) 'The legion vision of a worldwide virtual computer', Communications of the ACM, Vol. 40, No. 1, pp.39-45.
25. Judd, G., Clement, M. and Snell, Q. (1998) 'DOGMA: distributed object group metacomputing architecture', Concurrency: Practice and Experience, Vol. 10, No. 1, pp.1-7.
26. Leitner, T. (2002) The Molecular Epidemiology of Human Viruses, Kluwer Academic Publishers, Norwell, Massachusetts.
27. Maddison, W. and Maddison, D. (2003) Mesquite: A Modular System for Evolutionary Analysis, http://mesquiteproject.org
28. Microsoft Corporation (2003) Microsoft Netmeeting, http://www.microsoft. com/windows/netmeeting.
29. Morell, V. (1996) TreeBASE: the roots of phylogeny', Science, Vol. 273, p.569.
30. Napster (2003) http://www.napster.com.
31. Peterson, L. and Davie, B. (2000) Computer Networks: A Systems Approach, Morgan Kaufman publishers, San Francisco, California.
32. Piel, W., Donoghue, M. and Sanderson, M. (1996) 'TreeBASE: a relational database of phylogenetic information', Proceedings of the International Joint Workshop for Studies on Biodiversity, Tsubkuba, Japan, pp.41-47.
33. Semple, C. and Steel, M. (2003) Phylogenetics, Oxford University Press, Oxford.
34. Snell, Q., Tew, K., Ekstrom, J. and Clement, M. (2002) 'An enterprise based grid resource management system', Proceedings of the Eleventh IEEE International Symposium on High Performance Distributed Computing(HPDC-11), Edinburgh, Scotland, pp.83-92.
35. SourceForge (2003) http://sourceforge.net/
36. University of Cambridge (2003) Virtual Network Computing (VNC), http://www.uk.research.att.com/vnc