Large-scale co-phylogenetic analysis on the grid

International Journal of Grid and High Performance Computing

Volumn 1, Issue 1, 2009, Pages 39-54

  Stockinger, Heinz ^a   Auch, Alexander F ^b   Göker, Markus ^b   Jan, M K ^b   Stamatakis, Alexandros ^c  

^a SWISS INSTITUTE OF BIOINFORMATICS   (Switzerland)

^b UNIVERSITY OF TÜBINGEN   (Germany)

^c UNIVERSITY OF MUNICH   (Germany)

Author keywords

Bioinformatics; Co phylogenetic analysis; Grid computing; Phylogeny

Indexed keywords

BIOINFORMATICS; BIOLOGY;

COMPUTATIONAL GRIDS; HIGH-PERFORMANCE TECHNOLOGIES; LARGE-SCALE ANALYSIS; LARGE-SCALE DATA ANALYSIS; PHYLOGENETIC ANALYSIS; PHYLOGENETIC STUDIES; PHYLOGENY; STATISTICAL FRAMEWORK;

GRID COMPUTING;

EID: 77957243005     PISSN: 19380259     EISSN: 19380267     Source Type: Journal    
DOI: 10.4018/jghpc.2009010104     Document Type: Article

References (24)

1. Altschul, S.F., Madden, T.L., Schaffer, A.A., et al. (1997). Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Research, 25(17):3389-3402.
2. Chor, B., & Tuller, T. (2005). Maximum likelihood of evolutionary trees: hardness and approximation. Bioinformatics, 21(1):97-106.
3. Goloboff, P. (1999). Analyzing Large Data Sets in Reasonable Times: Solutions for Composite Optima. Cladistics 15(4): 415-428.
4. Charleston, M.A., & Perkins L. (2006). Traversing the tangle: Algorithms and applications for cophylo-genetic studies. Journal of Biomedical Informatics, 39 (2006):62-71.
5. Gottschling, M., Stamatakis, A., Nindl, I., et al. (2007). Multiple Evolutionary Mechanisms Drive Papillomavirus Diversification. Molecular Biology and Evolution, 24(5):1242-1258.
6. Hansen, H., Bachmann, L., & Bakke, T.A. (2003). Mitochondrial DNA variation of Gyrodactylus spp. Monogenea, Gyrodactylidae populations infecting Atlantic salmon, grayling, and rainbow trout in Norway and Sweden. International Journal of Parasitology, 33(13): 1471-1478.
7. Heinicke, M.P., Duellman, W.E., & Hedges, S.B. (2007). From the Cover: Major Caribbean and Central American frog faunas originated by ancient oceanic dispersal. Proceedings of the National Academy of Sci
8. Laure, E., Fisher, S., Frohner, A., et al. (2006). Programming the Grid with gLite. Computational Methods in Science and Technology, 12(1):33-45.
9. Legendre, P., Anderson, M.J. (1998). DistPCOA program description, source code, executables, and documentation: http://www.bio.umontreal.ca/Cas-grain/en/ labo/distpcoa.html
10. Legendre, P., Desdevises, Y., & Bazin, E. (2002). A Statistical Test for Host-Parasite Coevolution. Systematic Biology, 51(2):217-234.
11. Meier-Kolthoff, J.P, Auch, A.F., Huson, D.H., & Göker, M.(2007). COPYCAT: Co-phylogenetic Analysis tool. Bioinformatics, 23(7):898-900.
12. Meinilä, M., Kuusela, J., Zietara, M.S., & Lumme, J. (2004). Initial steps of speciation by geographic isolation and host switch in salmonid pathogen Gy- rodactylus salaris (Monogenea: Gyrodactylidae). International Journal of Parasitology, 34(4):515-526
13. Merkle, D., & Middendorf. M. (2005). Reconstruction of the cophylogenetic history of related phylo-genetic trees with divergence timing information. Theory in Biosciences, 123(4):277-299.
14. Ricklefs, R.E., Fallon, S.M., & Birmingham, E. (2004). Evolutionary relationships, cospeciation, and host switching in avian malaria parasites. Systematic Biology, 53(1):111-119.
15. Ronquist, F., & Huelsenbeck, J. (2003). MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics, 19(12): 1572-1574.
16. Salzberg, S.L., Kingsford, C., Cattoli, G., et al. (2007). Genome analysis linking recent European and African influenza (H5N1) viruses. Emerg Infect Dis,. 13(5):713-8.
17. Stamatakis, A. (2006). RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics, 22(21): 2688-2690.
18. Stamatakis, A., Hoover, P., & Rougemont, J. (2008). A Rapid Bootstrapping Algorithm for the RAxML Web Servers. Systematic Biology, in press.
19. Stamatakis, A., Auch, A.F., Meier-Kolthoff, J., & Göker, M. (2007). AxPcoords & parallel AxParafit: statistical co-phylogenetic analyses on thousands of taxa. BMC Bioinformatics 2007, 8:405.
20. Stockinger, H., Pagni, M., Cerutti, L., & Falquet, L. (2006). Grid Approach to Embarrassingly Parallel CPU-Intensive Bioinformatics Problems. 2nd IEEE International Conference on e-Science and Grid Computing (e-Science 2006), IEEE Computer Society Press, Amsterdam, The Netherlands.
21. Thomas, P.L., & Menzies, J.G. (1997). Cereal smuts in Manitoba and Saskatchewan, 1989-95. Canadian Journal of Plant Pathology, 19(2):161-165.
22. Thompson, J.D., Higgins, D.G., & Gibson, T.J. (1994). CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Research, 22(22):4673-4680.
23. de Vienne, D.M., Giraud, T., & Martin, O.C. (2007). A congruence index for testing topological similarity between trees. Bioinformatics, 23(23):3119-3124.
24. Zwickl, D. (2006). Genetic algorithm approaches for the phylogenetic analysis of large biological sequence datasets under the maximum likelihood criterion. PhD Thesis, The University of Texas at Austin.