Bioinformatics Advance Access originally published online on July 19, 2005
Bioinformatics 2005 21(19):3801-3802; doi:10.1093/bioinformatics/bti590
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Phylogenetic trees: visualizing, customizing and detecting incongruence
1Laboratorium for Bioinformatics and Computational Genomics (BioBix), Department of Molecular Biotechnology, Faculty of Bioscience Engineering, Ghent University Ghent, Belgium
2GenOhm Waarloos, Belgium
*To whom correspondence should be addressed.
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Abstract |
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 TOP Abstract 1 INTRODUCTION2 FEATURESREFERENCES |
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Summary: TreeIllustrator is a user-friendly application to visualize and customize phylogenetic trees. It has a broad range of functions and capabilities, such as dragging of nodes, different tree shapes, zooming and searching capabilities, and support for large trees. It acts as a solution that integrates the specificity of visualizing phylogenetic trees and the customization options of a drawing program. It also contains a simple and effective method that compares a custom tree with the Tree of Life, by detecting incongruence.
Availability: A free version is available online at http://nexus.ugent.be/geert/
Contact: wim.vancriekinge{at}ugent.be
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1 INTRODUCTION |
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TOPAbstract1 INTRODUCTION2 FEATURESREFERENCES |
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Visualization of phylogenetic trees is not merely an aesthetic point. A clear, interpretable visual representation of a tree is essential to gain information about the relationships between genes or species. Tree drawing programs are mostly specialized in a specific task of tree visualization: TreeView (Page, 1996) has a large amount of tree shapes, HyperTree (Bingham and Sudarsanam, 2000) lets you search nodes in big trees and has limited zooming capabilities, TreeTool (Maciukenas, 1994) (http://www.rfcgr.mrc.ac.uk/Registered/Option/treetool.html) allows you to drag nodes and TreeJuxtaposer (Munzner et al., 2003) is a powerful tool that compares and handles very large trees. Nevertheless an all-in-one program was not really available until now.
Biologists are often interested in comparing an inferred tree with the current classification in the Tree of Life. An experienced biologist can do this ad hoc by examining a compact tree. Larger trees however are harder to examine, and an automated exhaustive search could be useful here.
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2 FEATURES |
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TOPAbstract1 INTRODUCTION2 FEATURESREFERENCES |
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2.1 Incongruence search
TreeIllustrator offers an exhaustive comparison of the inferred tree with a built-in database that holds the current Tree of Life of the National Center for Biotechnology Information (NCBI) (Wheeler et al., 2000). After appointing the taxonomical names to the leaves of the tree, the internal nodes are labeled and an incongruence search is performed that points out where the incongruence is situated in the tree and gives an indication of how severe this incongruence is. The algorithm that is used to perform this search examines the influence of removing a node on the classification of the internal branches. An element is congruent if its removal has no influence on the classification of its closest ancestor that holds a minimum of two branches. The results are visualized on the tree (Fig. 1) and a log file is generated.
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2.2 Visualizing and customizing trees
TreeIllustrator can (1) display large phylogenetic trees with thousands of leaves, but it can also display a tree with few elements, both in six different ways, thanks to a zoom with a magnification factor up to a 1000%. The drawing algorithm makes sure that overlapping, as a result of tree enlargement and label rotation techniques, never happens. (2) Dragging of internal and terminal nodes allows the user to extract important information. (3) Graphic adaptation is possible through coloring, labeling, renaming, adjusting line thickness, fonts, font size, line curving, node rotation, bootstrap and distance visualization and independent x and y scaling. (4) A search engine with regular expressions gives the user a fast way of finding nodes in a large tree. (5) Six different tree shapes can be displayed: phylogram, rectangular cladogram, radial view, radial logarithmic, slanted cladogram and radial cladogram. The latter is a novel representation, implemented in TreeIllustrator (Fig. 1). (6) TreeIllustrator imports files based on the Newick format, such as Paup* (Swofford, 2003) and Phylip (Felsenstein, 1993) output files. (7) The generated trees can be saved as postscript vector format, JPeg bitmap format, Newick format or can be printed. (8) Written in Java, TreeIllustrator is platform independent and runs on all machines with a Java interpreter version 1.4.2 or higher installed.
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Acknowledgments |
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We are grateful to E. J. M. Van Damme and W. Peumans for their valuable comments and suggestions. The authors are most grateful for helpful information from the advisor–coordinators of BioScope-IT, a Bioinformatics Service Project within the context of the Flemish Innovation Network funded by the ‘Instituut voor de aanmoediging van innovatie door Wetenschap en Technologie in Vlaanderen’ (IWT 040571 BIO-IT service project).
Conflict of Interest: none declared.
Received on June 7, 2005; revised on July 7, 2005; accepted on July 15, 2005
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REFERENCES |
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TOPAbstract1 INTRODUCTION2 FEATURESREFERENCES |
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Bingham, J. and Sudarsanam, S. (2000) Visualizing large hierarchical clusters in hyperbolic space. Bioinformatics, 16, 660–661
Felsenstein, J. (1993) PHYLIP (Phylogeny Inference Package) version 3.5c. , Seattle Distributed by the author Department of Genetics, University of Washington.
Maciukenas, M. (1994) http://iubio.bio.indiana.edu/soft/molbio/unix/treetool/user.manual.
Munzner, T., et al. (2003) TreeJuxtaposer: scalable tree comparison using Focus+Context with guaranteed visibility. ACM Trans. Graph., 22, 453–462[CrossRef].
Page, R.D.M. (1996) TREEVIEW: an application to display phylogenetic trees on personal computers. Comput. Appl. Biosci., 12, 357–358
Swofford, D.L. PAUP* Phylogenetic Analysis Using Parsimony (*and Other Methods), (2003) , Sunderland, MA Version 4 Sinauer Associates.
Wheeler, D.L., et al. (2000) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res., 28, 10–14
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