Abstract
Over recent years the field of phylogenetics has witnessed significant algorithmic and technical progress. A new class of efficient phylogeny programs allows for computation of large evolutionary trees comprising 500–1.000 organisms within a couple of hours on a single CPU under elaborate optimization criteria. However, it is difficult to extract the valuable information contained in those large trees without appropriate visualization tools. As potential solution we propose the application of treemaps to visualize large phylogenies (evolutionary trees) and improve knowledge-retrieval. In addition, we propose a hybrid tree/treemap representation which provides a detailed view of subtrees via treemaps while maintaining a contextual view of the entire topology at the same time. Moreover, we demonstrate how it can be deployed to visualize an evolutionary tree comprising 2.415 mammals. The respective software package is available on-line at www.ics.forth.gr/~stamatak.
Part of this work is funded by a Postdoc-fellowship granted by the German Academic Exchange Service (DAAD)
This work was supported in part by INFOBIOMED code: IST-2002-507585 and the Greek General Secretariat for Research and Technology under Program “ARISTEIA”, Code 1308/B1/3.3.1/317/12.04.2002
This is a preview of subscription content, log in via an institution to check access.
Preview
Unable to display preview. Download preview PDF.
Similar content being viewed by others
References
Bader, D.A., Moret, B.M.E., Vawter, L.: Industrial applications of highperformance computing for phylogeny reconstruction. In: Proceedings of SPIE ITCom: Commercial Applications for High-Performance Computing, pp. 159–168 (2001)
Berderson, B.B., Shneiderman, B., Wattenberg, M.: Ordered and quantum treemaps: Making effective use of 2d space to display hierarchies. ACM Transactions on Computer Graphics 21(4), 833–854 (2002)
Bingham, J., Sudarsanam, S.: Visualizing large hierarchical clusters in hyperbolic space. Bioinformatics 16, 660–661 (2000)
Bodlaender, H.L., Fellows, M.R., Hallett, M.T., Wareham, T., Warnow, T.: The hardness of perfect phylogeny, feasible register assignment and other problems on thin colored graphs. Theoretical Computer Science 244, 167–188 (2000)
Bruls, D.M., Huizing, C., van Wijk, J.J.: Squarified treemaps. In: Proceedings of the joint Eurographics and IEEE TVCG Symposium on Visualization, pp. 33–42 (2000)
Carrizo, S.F.: Phylogenetic trees: an information visualisation perspective. In: Proceedings of the second conference on Asia-Pacific bioinformatics, pp. 315–320 (2004)
Day, W.H.E., Johnson, D.S., Sankoff, D.: The computational complexity of inferring rooted phylogenies by parsimony. Math. Bios. 81, 33–42 (1986)
Chase, M.W., et al.: Phylogenetics of seed plants: An analysis of nucleotide sequences from the plastid gene rbcl. Annals of the Missouri Botanical Garden, 528–580 (1993)
Felsenstein, J.: Evolutionary trees from DNA sequences: A maximum likelihood approach. Journal of Molecular Evolution 17, 368–376 (1981)
Fitch, W.M.: Toward defining the course of evolution: minimum change for a specified tree topology. Syst. Zool. 20, 406–416 (1971)
Guindon, S., Gascuel, O.: A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52(5), 696–704 (2003)
Hughes, T., Hyun, Y., Liberles, D.A.: Visualizing very large phylogenetic trees in three dimensional hyperbolic space. BMC Bioinformatics 5(48) (2004)
Johnson, B., Shneiderman, B.: Treemaps: a space-filling approach to the visualization of hierarchical information structures. In: Proceedings of the 2nd International IEEE Visualization Conference, October 1991, pp. 284–291 (1991)
Leung, J.Y.T., Lam, T.W., Wong, C.S., Young, G.H., Chin, F.Y.L.: Packing squares into a square. Journal on Parallel and Distributed Compouting 10, 271–275 (1990)
Lemmon, A.R., Milinkovitch, M.C.: The metapopulation genetic algorithm: An efficient solution for the problem of large phylogeny estimation. Proceedings of the National Academy of Sciences 99, 10516–10521 (2001)
Munzner, T., Guimbretiere, F., Tasiran, S., Zhang, L., Zhou, Y.: Treejuxtaposer: Scalable tree comparison using focus+context with guaranteed visibility. In: Proceedings of SIGGRAPH (2003)
Page, R.D.M.: Treeview: An application to display phylogenetic trees on personal computers. CABIOS 12, 357–358 (1996)
Plaisant, C., Grosjean, J., Bederson, B.B.: Spacetree: Supporting exploration in large node link tree, design evolution and empirical evaluation. In: Proceedings of the 2002 IEEE Symposium on Information Visualization, pp. 57–70 (2002)
Roshan, U., Moret, B.M.E., Warnow, T., Williams, T.L.: Rec-i-dcm3: a fast algorithmic technique for reconstructing large phylogenetic trees. In: Proceedings of the IEEE Computational Systems Bioinformatics conference (CSB), Stanford, California, USA (2004)
Rost, U., Bornberg-Bauer, E.: Treewiz: interactive exploration of huge trees. Bioinformatics, 109–114 (2002)
Ruths, D.A., Chen, E.S., Ellis, L.: Arbor3d: an interactive environment for examining phylogenetic and taxonomic trees in multiple dimensions. Bioinformatics, 1003–1009 (2000)
Sanderson, M.J., Driskell, A.C.: The challenge of constructing large phylogenetic trees. Trends in Plant Science 8(8), 374–378 (2003)
Stamatakis, A.: An efficient program for phylogenetic inference using simulated annealing. In: Proceedings of IPDPS 2005, Denver, Colorado, USA (2005)
Stamatakis, A., Ludwig, T., Meier, H.: Parallel inference of a 10.000-taxon phylogeny with maximum likelihood. In: Proceedings of 10th International Euro Par Conference, pp. 997–1004 (2004)
Stamatakis, A., Ludwig, T., Meier, H.: Raxml-iii: A fast program for maximum likelihood-based inference of large phylogenetic trees. Bioinformatics 21(4), 456–463 (2005)
Stamatakis, A., Ott, M., Ludwig, T.: Raxml-omp: An efficient program for phylogenetic inference on smps. In: Proceedings of 8th International Conference on Parallel Computing Technologies, PaCT (2005), Preprint available on-line at www.ics.forth.gr/~stamatak
Stolk, B., Abdoelrahman, F., Koning, A., Wielinga, P., Neefs, J.M., Stubbs, A., de Bondt, A., Leemans, P., van der Spek, P.: Mining the human genome using virtual reality. In: Proceedings of the Fourth Eurographics Workshop on parallel Graphics and Visualization, pp. 17–21 (2002)
Tang, J., Moret, B.M.E., Cui, L., de Pamphilis, C.W.: Phylogenetic reconstruction from arbitrary gene-order data. In: Proc. 4th IEEE Conf. on Bioinformatics and Bioengineering BIBE 2004, pp. 592–599 (2004)
Zmasek, C.M., Eddy, S.R.: Atv: Display and manipulation of annotated phylogenetic trees. Bioinformatics 17, 383–384 (2001)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2005 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Arvelakis, A., Reczko, M., Stamatakis, A., Symeonidis, A., Tollis, I.G. (2005). Using Treemaps to Visualize Phylogenetic Trees. In: Oliveira, J.L., Maojo, V., Martín-Sánchez, F., Pereira, A.S. (eds) Biological and Medical Data Analysis. ISBMDA 2005. Lecture Notes in Computer Science(), vol 3745. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11573067_29
Download citation
DOI: https://doi.org/10.1007/11573067_29
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-29674-4
Online ISBN: 978-3-540-31658-9
eBook Packages: Computer ScienceComputer Science (R0)