A framework for large-scale interactive visualization of phylogenetic trees

Proceedings of the 6th IASTED International Conference on Visualization, Imaging, and Image Processing, VIIP 2006

Volumn , Issue , 2006, Pages 122-129

  Meyer, Joerg ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Immersive rendering; Information visualization; Interactive visualization; Large scale visualization; Phylogenetic trees; Web based rendering

Indexed keywords

DATA STRUCTURES; DIGITAL IMAGE STORAGE; IMAGE PROCESSING; IMAGING SYSTEMS; INFORMATION SYSTEMS;

IMMERSIVE RENDERING; INFORMATION VISUALIZATION; INTERACTIVE VISUALIZATION; LARGE-SCALE VISUALIZATION; PHYLOGENETIC TREES; WEB-BASED RENDERING;

VISUALIZATION;

EID: 56349139562     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: None     Document Type: Conference Paper

References (53)

1. Abiteboul, Serge; Quass, Dallan; McHugh, Jason; Widom, Jennifer; Wiener, Janet L.: The Lorel Query Language for Semistructured Data, Int. J. on Digital Libraries, Vol. 1, No. 1, pp. 68-88, 1997.
2. Ananthanarayanan, R.; Gottemukkala, Vibby; Kafer, Wolfgang; Lehman, Tobin J.; Pirahesh, Hamid: Using the Co-existence Approach to Achieve Combined Functionality of Object-Oriented and Relational Systems, Proceedings of the 1993 ACM SIGMOD International Conference on Management of Data, Washington, D.C., pp. 109/ 118, May 26-28, 1993.
3. Banchilhon, F.; Delobel, C.; Kanellakis, P.: Building an Object-Oriented Database System: The story of O2, Morgan Kaufmann, 1992.
4. Bininda-Emonds, Olaf R. P.; Bryant, Harold N.: Properties of matrix representation with parsimony analyses, Systematic Biology, Vol. 47, pp. 497-508, 1998.
5. Bowman, B. H.; Taylor, J. W.; White, T. J.: Molecular evolution of the fungi: human pathogens, Mol. Biol. Evol., Vol. 9, pp. 893-904, 1992.
6. Buneman, Peter; Davidson, Susan B.; Hillebrand, Gerd G.; Suciu, Dan: A Query Language and Optimization Techniques for Unstructured Data, SIGMOD Conference, pp. 505-516, 1996.
7. Cavalli-Sforza, L. L.; Edwards, A. W. F.: Analysis of human evolution. Proc. 11th Intl. Congress Genet., pp. 923-933, 1964.
8. Clark, J.: XSL transformations, Version 1.0, http://www.w3.org/TR/WD- xslt, August 1999.
9. Colby, L. S.: A Recursive Algebra and Query Optimization for Nested Relations, Proceedings of the ACM SIGMOD, pp. 273-283, 1989.
10. Crandall, K. (ed.): The evolution of HIV, Johns Hopkins, Baltimore, 1999.
11. Deutsch, Alin; Fernandez, Mary F.; Florescu, Daniela; Levy, Alon Y.; Suciu, Dan: A Query Language for XML, Proc. of WWW8 Conference, 1999.
12. Eulenstein, Oliver; Mirkin, Boris; Vingron, Martin: Comparison of Annotation Duplication, Tree Mapping, and Copying as Methods to Compare Gene Trees with Species Trees, DIMACS Series in Discrete Mathematics and Theoretical Computer Sciences, AMS, Vol. 37, pp. 71-93, 1997.
13. Eulenstein, Oliver; Mirkin, Boris; Vingron, Martin: Duplication-Based Measures of Difference Between Gene- and Species Trees, Journal of Computational Biology, Vol. 5, pp. 135-148, 1998.
14. Fernandez, Mary F.; Florescu, Daniela; Kang, Jaewoo; Levy, Alon Y.; Suciu, Dan: Catching the Boat with Strudel: Experiences with a Web-Site Management System, SIGMOD Conference, pp. 414-425, 1998.
15. Hamann, B.: A data reductions scheme for triangulated surfaces, Computer Aided Geometric Design, Vol. 11, No. 2, pp. 197-214, 1994.
16. Herman, I; Melancon, G.; Marshall, M. S.: Graph Visualization and Navigation in Information Visualization: A Survey, Transactions on Visualization and Computer Graphics, Vol 6, No. 1, January-March 2000.
17. Hillis, D. M: Taxonomic sampling, phylogenetic accuracy, and investigator bias, Systematic Biololgy, Vol. 47, pp. 3-8, 1998.
18. Holmes, E. C.: Using phylogenetic trees to reconstruct the history of infectious disease epidemics, in Harvey, P. H. et al. (ed.): New uses for new phylogenies, Oxford University Press, Oxford, England, UK, New York, New York, USA, pp. 169-186, 1996.
19. Jamil, H. M.; Lakshmanan, L. V. S.: A Declarative Semantics for Behavioral Inheritance and Conflict Resolution, in Lloyd, John (ed.): Proceedings of the 12th International Logic Programming Symposium (ILPS), Portland, Oregon, MIT Press, pp. 130-144, December 4-7, 1995.
20. Jamil, H. M.: GQL: A Reasonable Complex SQL for Genomic Databases, IEEE International Symposium on BioInformatics and Biomedical Engineering (BIBE 2000), Washington D.C., USA, November 8-10, 2000.
21. Keller, Arthur M.; Jensen, Richard; Agrawal, Shailesh: Proceedings of the 1993 ACM SIGMOD International Conference on Management of Data, Washington, D.C., pp. 523-528, May 26-28, 1993.
22. Kifer, M.; Lausen, G.; Wu, J.: Logical Foundations for Object-Oriented and Frame-Based Languages, Journal of the Association of Computing Machinery, Vol. 42, No. 3, pp. 741-843, 1995.
23. Koike, H.; Yoshihara, H.: Fractal Approaches for Visualizing Huge Hierarchies, Proceedings of the 1993 IEEE Symposium on Visual Languages, pp. 55-60, IEEE/CS, 1993.
24. Korber, B.; Hahn, B.; Foley, B.; Mellors, J. W.; Leitner, T.; Myers, G.; McCutchan, F.; Kuiken, C. L. (eds.): Human Retroviruses and AIDS: A Compilation and Analysis of Nucleic Acid and Amino Acid Sequences, Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM, 1997.
25. Korber, B.; Muldoon, M.; Theiler, J. et al.: Timing the ancestor of HIV-1 pandemic strains, Science, Vol. 288, pp. 1789-1796, 2000.
26. Lanciotti, R. S.; Roehrig, , J. T.; Deubel, V. et al.: Origin of the West Nile virus responsible for an outbreak of encephalitis in the Northeastern United States, Science, Vol. 286, pp. 2333-2337, 1999.
27. Lathe, W. C. III; Burke, W. D.; Eickbush, D. G.; Eickbush, T. H.: Evolutionary stability of the R1 retrotransposable element in the genus Drosophila, Molecular Biology and Evolution, Vol. 12, pp. 1094-1105, 1995.
28. Maier, D.: The Theory of Relational Databases, Computer Science Press, MD, 1993.
29. McGuire, K.; Holmes, E. C.; Gao, G. F.; Reid, H. W.; Gould, E. A.: Tracing the origins of louping ill virus by molecular phylogenetic analysis, Journal of General Virology, Vol. 79, pp. 981-988, 1998.
30. Meyer, Joerg: Interactive Rendering of Medical and Biological Data Sets; Ph. D. thesis; Department of Computer Science, University of Kaiserslautern, Germany, Shaker Verlag, September 29, 1999 (ISBN 3-8265-7009-X).
31. Meyer, Joerg; Borg, Ragnar; Hamann, Bernd: VR-based Rendering Techniques for Time-Critical Applications; Scientific Visualization 2000, Schloss Dagstuhl, Germany, accepted for publication, May 22-26, 2000.
32. Mindell, D. P.; Shultz, J. W.; Ewald, P. W.: The AIDS pandemic is new but is HIV new?, Systematic Biology, Vol. 44, pp. 77-92, 1995.
33. Munzner, Tamara: Exploring Large Graphs in 3D Hyperbolic Space, IEEE Computer Graphics and Applications, Vol. 18, No. 4, pp. 18-23, July/August 1998.
34. Nadeau, David R.; Baley, Michael J.: Visualizing Volume Data using Physical Models, IEEE Visualization Conference, pp. 49-50, 2000.
35. Ou, C.-Y. et al.: Molecular epidemiology of HIV transmission in a dental practice, Science, Vol. 256, pp. 1165-1171, 1992.
36. Van de Peer, Y.; Rensing, S. A.; Maier, U.-G.; de Wachter, R.: Substitution rate calibration of small subunit ribosomal RNA identifies chlorarachniophyte endosymbionts as remnants of green algae, Proc. Natl. Acad. Sci., Vol. 93, pp. 7732-7736, 1996.
37. Van de Peer, Y.; de Wachter, R.: Evolutionary relationships among the eukaryotic crown taxa taking into account site-to-ste rate variation in 18S rRNA, J. Mol. Evol., Vol. 45, pp. 619-630, 1997.
38. Rich, S. M.; Licht, M. C.; Hudson, R. R.; Ayala, F. J.: Malaria's eve: evidence for a recent population bottleneck throughout the world's populations of Plasmodium falciparum, Proc. Natl. Acad. Sci., USA, Vol. 95, pp. 4425-4430, 1998.
39. Rijk, P.; van de Peer, Y; de Wachter, R.: The rRNA WWW Server. Univ Of Antwerp, 1998.
40. Robie, J.: The design of XQL, http://www.texcel.no/whitepapers/xql- design.html, 1999.
41. Sanderson, Michael J.; Purvis, Andy; Henze, Chris: Phylogenetic supertrees: assembling the tree of life, Trends in Ecology & Evolution, Vol. 13, No. 3, pp. 105-109, March 1998.
42. Semple, Charles; Steel, Mike: A supertree method for rooted trees, Discrete Applied Mathematics, Vol. 105, pp. 147-158, 2000.
43. Silberschatz, A.; Korth, H. F.; Sudarshan, S.: Database System Concepts (Third Edition), McGraw-Hill, 1996.
44. Snodgrass, Richard T.; Winslett, Winslett: UniSQL/X Unified Relational and Object-Oriented Database System, Proceedings of the 1994 ACM SIGMOD International Conference on Management of Data, Minneapolis, Minnesota, p. 481, May 24-27, 1994.
45. Steel, Mike: The complexity of reconstructing trees from qualitative characters and subtrees, Journal of Classification, Vol. 9, pp. 91-116, 1992.
46. Swofford, D. L.: When are phylogeny estimates from molecular and morphological data incongruent? in Miyamoto, M. M.; Cracraft, J. (eds.): Phylogenetic analysis of DNA sequences, Oxford University Press, New York, pp. 295-333, 1991.
47. Teuhola, Jukka: An Efficient Relational Implementation of Recursive Relationships using Path Signatures, Proceedings of the Tenth International Conference on Data Engineering, Houston, Texas, pp. 348-355, February 14-18, 1994.
48. Ullman, J. D.: Principles of Database and Knowledge-base Systems, Part I and II, Computer Science Press, 1988.
49. Wade, C. M.; Lobidel, D.; Leigh Brown, A. J.: Analysis of human immunodeficiency virus type 1 env and gag sequence variants derived from a mother and two vertically infected children provides evidence for the transmission of multiple sequence variants, J. Gen. Virol., Vol. 79, pp. 1055-1068, 1998.
50. Wilkie, T. M.; Yokoyama, S.: Evolution of the G protein alpha subunit multigene family, in Fambrough, D. M. (ed.): Molecular evolution of physiological processes, Rockefeller Univ. Press, New York, pp. 249-270, 1994.
51. Yuan, Yan P.; Eulenstein, Oliver; Vingron, Martin; Bork, Per: Towards detection of orthologues in sequence databases, Bioinformatics, Vol. 14, No. 3, pp. 285-289, 1998.
52. Zuckerkandl, E.; Pauling, L.: Molecular disease, evolution, and genetic heterogeneity, in Kasha, M.; Pullman, B. (eds.): Horizons in biochemistry, Academic Press, New York, pp. 189-225, 1962.
53. Zuckerkandl, E.; Pauling, L.: Evolutionary divergence and convergence, in Bryson, V.; Vogel, H. J. (eds.): Evolving genes and proteins, Academic Press, New York, pp. 97-166, 1965.