Interactive visual comparison of multiple trees

VAST 2011 - IEEE Conference on Visual Analytics Science and Technology 2011, Proceedings

Volumn , Issue , 2011, Pages 31-40

  Bremm, Sebastian ^a   Von Landesberger, Tatiana ^a   Hess, Martin ^a   Schreck, Tobias ^b   Weil, Philipp ^a   Hamacherk, Kay ^a  

^a DARMSTADT UNIVERSITY OF TECHNOLOGY   (Germany)

^b UNIVERSITY OF KONSTANZ   (Germany)

Author keywords

I.3.3 Computer Graphics : Viewing Algorithms H.5.2 : User Interfaces (D.2.2, H.1.2, I.3.6) Interaction styles (e.g., commands, menus, forms, direct manipulation); I.3.6 Computer Graphics : Methodology and Techniques Graphics data structures and data types

Indexed keywords

16S RIBOSOMAL RNA; DATA SETS; EVOLUTIONARY BIOLOGY; EVOLUTIONARY PROCESS; EVOLUTIONARY RELATIONSHIPS; I.3.6 [ COMPUTER GRAPHICS]: METHODOLOGY AND TECHNIQUES - GRAPHICS DATA STRUCTURES AND DATA TYPES; INPUT DATAS; LEVELS OF DETAIL; LOCAL STRUCTURE; MULTIPLE TREES; PHYLOGENETIC TREES; PROTEIN SEQUENCES; RESEARCH AREAS; SIMULTANEOUS ANALYSIS; STATISTICAL SIGNIFICANCE; TREE COMPARISON; VIEWING ALGORITHMS; VISUAL ANALYSIS; VISUAL ANALYTICS; VISUAL COMPARISON;

BIOLOGY; DATA STRUCTURES; GRAPHICAL USER INTERFACES; INTERACTIVE COMPUTER GRAPHICS; RNA; TECHNOLOGY; VISUALIZATION;

FORESTRY;

COMPUTER GRAPHICS; DATA PROCESSING; GRAPHICAL USER INTERFACES; HIERARCHICAL SYSTEMS;

EID: 84855780787     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/VAST.2011.6102439     Document Type: Conference Paper

References (39)

1. M. Anisimova and O. Gascuel. Approximate likelihood-ratio test for branches: A fast, accurate, and powerful alternative. Systematic Biology, 55(4):539-552, Aug. 2006. PMID: 16785212. (Pubitemid 43922340)
2. C. Appert and J.-D. Fekete. Naviguer dans des grands arbres avec controltree. In Proceedings of International Conference of the Association Francophone d'Interaction Homme-Machine, pages 139-142, 2007.
3. S. K. Card and D. Nation. Degree-of-interest trees: a component of an attention-reactive user interface. In AVI '02: Proceedings of theWorking Conference on Advanced Visual Interfaces, pages 231-245, New York, NY, USA, 2002. ACM.
4. J. Castresana. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Molecular Biology and Evolution, 17(4):540-552, Apr. 2000. PMID: 10742046. (Pubitemid 30210700)
5. J. Chen, A. MacEachren, and D. Peuquet. Constructing Overview+ Detail Dendrogram-Matrix Views. Visualization and Computer Graphics, IEEE Transactions on, 15(6):889-896, 2009.
6. P. J. A. Cock, T. Antao, J. T. Chang, B. A. Chapman, C. J. Cox, A. Dalke, I. Friedberg, T. Hamelryck, F. Kauff, B. Wilczynski, and M. J. L. de Hoon. Biopython: freely available python tools for computational molecular biology and bioinformatics. Bioinformatics (Oxford, England), 25(11):1422-1423, June 2009. PMID: 19304878.
7. A. Dereeper, V. Guignon, G. Blanc, S. Audic, S. Buffet, F. Chevenet, J. Dufayard, S. Guindon, V. Lefort, M. Lescot, J. Claverie, and O. Gascuel. Phylogeny.fr: robust phylogenetic analysis for the non-specialist. Nucleic Acids Research, 36(Web Server):W465-W469, 2008.
8. R. C. Edgar. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research, 32(5):1792 -1797, Mar. 2004.
9. N. Elmqvist and J.-D. Fekete. Hierarchical aggregation for information visualization: Overview, techniques, and design guidelines. IEEE Transactions on Visualization and Computer Graphics, 99, 2009.
10. R. D. Finn, J. Tate, J. Mistry, P. C. Coggill, S. J. Sammut, H. Hotz, G. Ceric, K. Forslund, S. R. Eddy, E. L. L. Sonnhammer, and A. Bateman. The pfam protein families database. Nucleic Acids Research, 36(Database):D281-D288, 2007.
11. M. Freire, C. Plaisant, B. Shneiderman, and J. Golbeck. ManyNets: an interface for multiple network analysis and visualization. In Proceedings of international conference on Human factors in computing systems, pages 213-222, New York, NY, USA, 2010. ACM.
12. M. Graham and J. Kennedy. A survey of multiple tree visualisation. Information Visualization, 9(4):235-252, 2009.
13. S. Guindon and O. Gascuel. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Systematic Biology, 52(5):696-704, Oct. 2003. PMID: 14530136. (Pubitemid 37365050)
14. K. Hamacher. Protein domain phylogenies - information theory and evolutionary dynamics. In A. Fred, J. Filipe, and H. Gamboa, editors, Bioinformatics, pages 114-122, 2010.
15. J. Heer and S. K. Card. Doitrees revisited: scalable, space-constrained visualization of hierarchical data. In AVI '04: Proceedings of the working conference on Advanced visual interfaces, pages 421-424, New York, NY, USA, 2004. ACM.
16. D. Hillis, T. Heath, and K. John. Analysis and visualization of tree space. Systematic Biology, 54(3):471, 2005.
17. D. Holten and J. Van Wijk. Visual comparison of hierarchically organized data. Computer Graphics Forum, 27(3):759-766, 2008.
18. N. Hulo, A. Bairoch, V. Bulliard, L. Cerutti, B. A. Cuche, E. de Castro, C. Lachaize, P. S. Langendijk-Genevaux, and C. J. A. Sigrist. The 20 years of PROSITE. Nucleic Acids Research, 36(Database issue):D245-D249, Jan. 2008. PMID: 18003654 PMCID: 2238851. (Pubitemid 351149730)
19. D. Huson, D. Richter, C. Rausch, T. Dezulian, M. Franz, and R. Rupp. Dendroscope: An interactive viewer for large phylogenetic trees. Bmc Bioinformatics, 8(1):460, 2007.
20. Institute of Evolutionary Biology, University of Edinburgh. Figtree. http://tree.bio.ed.ac.uk/software/figtree/.
21. D. Keim, T. Ertl, H. Ritter, G. Weikum, and S. Wrobel. Strategic Research Initiative 1335: Scalable Visual Analytics - Interactive Visual Analysis Systems of Complex Information Spaces. http: //www.visualanalytics.de/.
22. I. Letunic and P. Bork. Interactive tree of life (itol): an online tool for phylogenetic tree display and annotation. Bioinformatics, 23(1):127, 2006.
23. M. Li, J. Badger, C. Xin, S. Kwong, and P. e. Kearney. An information based sequence distance and its application to whole mitochondrial genome phylogeny. Bioinformatics, 17:149-154, 2001. (Pubitemid 32208523)
24. Y. Lin and T. Hsu. Efficient algorithms for descendent subtrees comparison of phylogenetic trees with applications to co-evolutionary classifications in bacterial genome. Algorithms and Computation, pages 339-351, 2003.
25. Y.-L. Lin and T.-S. Hsu. Efficient algorithms for descendent subtrees comparison of phylogenetic trees with applications to co-evolutionary classifications in bacterial genome. In T. Ibaraki, N. Katoh, and H. Ono, editors, Algorithms and Computation, volume 2906 of Lecture Notes in Computer Science, pages 339-351. Springer Berlin / Heidelberg, 2003.
26. M. Löbrich and G. Thiel. DFG Graduiertenkolleg 1657 "Molecular and cellular reactions on ionizing radiation" . http://www.grk1657.de/.
27. T. Munzner, F. Guimbretière, S. Tasiran, L. Zhang, and Y. Zhou. Tree-juxtaposer: scalable tree comparison using focus+context with guaranteed visibility. ACM Trans. Graph., 22:453-462, July 2003.
28. T. Nye. Trees of trees: an approach to comparing multiple alternative phylogenies. Systematic biology, 57(5):785, 2008.
29. S. Pape, F. Hoffgaard, and K. Hamacher. Distance-dependent classification of amino acids by information theory. Proteins: Structure, Function, and Bioinformatics, 78(10):2322-2328, 2010.
30. P. Puigbo, S. Garcia-Valle, and J. O. McInerney. TOPD/FMTS: a new software to compare phylogenetic trees. Bioinformatics, 23(12):1556-1558, June 2007. (Pubitemid 47244483)
31. B. Shneiderman. Tree visualization with tree-maps: 2-d space-filling approach. ACM Transactions on graphics (TOG), 11(1):92-99, 1992.
32. M. Steel and D. Penny. Distributions of tree comparison metrics-some new results. Systematic Biology, 42(2):126-141, 1993.
33. A. Telea and D. Auber. Code flows: Visualizing structural evolution of source code. In Computer Graphics Forum, volume 27, pages 831-838. Wiley Online Library, 2008.
34. Y. Tu and H. Shen. Visualizing changes of hierarchical data using treemaps. IEEE Transactions on Visualization and Computer Graphics, pages 1286-1293, 2007. (Pubitemid 350076601)
35. Y. Tu and H.-W. Shen. Balloon focus: a seamless multi-focus+context method for treemaps. Visualization and Computer Graphics, IEEE Transactions on, 14(6):1157-1164, Nov.-Dec. 2008.
36. T. von Landesberger, M. Görner, and T. Schreck. Visual analysis of graphs with multiple connected components. In Proceedings of IEEE Symposium on Visual Analytics Science and Technology, pages 155-162, 2009.
37. T. von Landesberger, A. Kuijper, T. Schreck, J. Kohlhammer, J. van Wijk, J.-D. Fekete, and D. Fellner. Visual analysis of large graphs: State-of-the-art and future research challenges. Computer Graphics Forum, pages no-no, 2011.
38. D. Wu, P. Hugenholtz, K. Mavromatis, R. Pukall, E. Dalin, N. N. Ivanova, V. Kunin, L. Goodwin, M. Wu, B. J. Tindall, S. D. Hooper, A. Pati, A. Lykidis, S. Spring, I. J. Anderson, P. Dhaeseleer, A. Zemla, M. Singer, A. Lapidus, M. Nolan, A. Copeland, C. Han, F. Chen, J.-F. Cheng, S. Lucas, C. Kerfeld, E. Lang, S. Gronow, P. Chain, D. Bruce, E. M. Rubin, N. C. Kyrpides, H.-P. Klenk, and J. A. Eisen. A phylogeny-driven genomic encyclopaedia of bacteria and archaea. Nature, 462:1056 - 1060, 2009.
39. Y. Zhong, C. Meacham, and S. Pramanik. A general method for tree-comparison based on subtree similarity and its use in a taxonomic database. Biosystems, 42(1):1-8, 1997 (Pubitemid 27193033)