Author Topic: Dendroscope 2 is an interactive viewer for large phylogenetic trees and networks  (Read 3081 times)

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Dendroscope 2 is a cross platform interactive viewer for large phylogenetic trees and networks.

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Citing:  Dendroscope: An interactive viewer for large phylogenetic trees
by Daniel H Huson, Daniel C Richter, Christian Rausch, Tobias Dezulian, Markus Franz and Regula Rupp at the Center for Bioinformatics Tübingen (ZBIT), Eberhard-Karls-Universität Tübingen, Sand 14, 72076 Tübingen, Germany


Abstract

Background

Research in evolution requires software for visualizing and editing phylogenetic trees, for increasingly very large datasets, such as arise in expression analysis or metagenomics, for example. It would be desirable to have a program that provides these services in an effcient and user-friendly way, and that can be easily installed and run on all major operating systems. Although a large number of tree visualization tools are freely available, some as a part of more comprehensive analysis packages, all have drawbacks in one or more domains. They either lack some of the standard tree visualization techniques or basic graphics and editing features, or they are restricted to small trees containing only tens of thousands of taxa. Moreover, many programs are diffcult to install or are not available for all common operating systems.

Results

We have developed a new program, Dendroscope, for the interactive visualization and navigation of phylogenetic trees. The program provides all standard tree visualizations and is optimized to run interactively on trees containing hundreds of thousands of taxa. The program provides tree editing and graphics export capabilities. To support the inspection of large trees, Dendroscope offers a magnification tool. The software is written in Java 1.4 and installers are provided for Linux/Unix, MacOS X and Windows XP.

Conclusion

Dendroscope is a user-friendly program for visualizing and navigating phylogenetic trees, for both small and large datasets.

Background

Phylogenetic trees are used to represent evolutionary relationships between biological taxa, while taxonomical hierarchies such as the NCBI taxonomy are used to structure the wealth of molecular sequence data. The size of trees under consideration is growing larger and larger.

The Tree of Life project, which aims at reconstructing the evolutionary relationship of all living species on earth, now considers more than 11,000 species. The Ribosomal Database Project II provides a hierarchical browser for a collection of approximately 340,000 ribosomal RNA sequences. Recent metagenomic analysis software makes use of the full NCBI taxonomy, which now contains more than 390,000 taxa, to estimate the taxonomical content of a dataset.

Most currently available tree viewers are designed to handle trees containing up to a few thousand nodes. A notable exception is TreeJuxtaposer, which was explicitly designed to visualize large trees. While TreeJuxtaposer is the tool of choice for very large datasets (containing hundreds of thousands of taxa), it has limited value as an all-round tree visualization tool, as it only implements one particular tree view (namely the rectangular phylogram, perhaps because this is the only view that is useful for large trees), it lacks basic graphics export capabilities and it does not allow one to save and reopen a modified tree.

Results and Discussion

Dendroscope is designed as an all-round tree visualization tool that can handle trees with hundred thousands of taxa. Trees can be read and written in Newick or Nexus format, as produced by standard tree reconstruction programs. Additionally, Dendroscope uses its own file format to save and reopen (lists of) trees that have been edited graphically using different colors, line widths and fonts.

Requires a Free License Key.
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Licence key for Dendroscope

Welcome to the Dendroscope registration site.
Each user of Dendroscope is required to obtain their own personal license-key for using the program. This is because we would like to known who is using our program. This data will only be used for statistical purposes and will not be made available to third parties. Also, we will not send you any email unless you select "Please inform me about Dendroscope updates", in which case we will do just that.

License-keys are issued free-of-charge to all users. Simply use the form to request a license-key from our server.

Please enable cookies or pressing the "Request Key" button may cause an error.


Software Santa got HIS Copy ....

http://www-ab.informatik.uni-tuebingen.de/data/software/dendroscope/download/welcome.html

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Dendroscope 2 - An interactive viewer for large phylogenetic trees and networks

Researchers studying phylogenetic relationships need software that is able to visualize rooted phylogenetic trees and networks efficiently, increasingly of large datasets involving hundreds of thousands of taxa. The program should be user friendly (easy to run on all popular operating systems), facilitate interactive browsing and editing the trees and allow one to export the result in multiple file formats in publication quality.

We have developed the platform independent tree and rooted network viewer Dendroscope that addresses these issues.

Feature List:

    * Large trees with hundreds of thousands of taxa can be easily displayed, browsed and edited;
    * Novel magnifying features for zooming detailed views (see screenshots);
    * Find and replace dialog that uses regular expressions;
    * Subtrees can be collapsed and colored;
    * All labels (leaves/inner nodes and edges) can be edited;
    * Trees can be rerooted;
    * Seven different views are available, including a rectangular, slanted, circular and radial view;
    * Input formats: Newick and Nexus, extended-Newick (for rooted phylogenetic networks) and Dendroscope;
    * Multiple graphic export formats: .eps, .svg, .png, .jpg, .gif, .bmp, .pdf;
    * Trees and networks can be copied and pasted between different windows
    * Platform independent (Java, installers for common operating systems available)
    * Consensus trees and rooted phylogenetic networks can be computed from a set of trees
    * Commandline mode

Download

Use of the program requires a  license. Academic licenses are freely available to all academic users. Usage in non-academic settings requires a free commerical license. All uses of the program must be acknowledged by citing our paper on Dendroscope.

Obtain a license key online.

Download an installer for linux, MacOS X or Windows here.

You can test the performance of the program on the NCBI taxonomy.

References

    * Daniel H Huson, Daniel C Richter, Christian Rausch, Tobias Dezulian, Markus Franz and Regula Rupp. Dendroscope: An interactive viewer for large phylogenetic trees, BMC Bioinformatics. 2007 Nov 22;8(1):460  (Here you can find Table 1 from the paper in case it is wrongly displayed in the pdf or at the BMC webpage.)

The new network capabilities introduced in version 2.0 are based on the following papers:

    * D.H. Huson and R. Rupp, Summarizing Multiple Gene Trees using Cluster Networks, WABI 2008, 295-305.
    * D.H. Huson, Drawing Rooted Phylogenetic Networks, TCBB, Jan-March 2009, Vol.6, Issue 1, pages 103-109.
    * D. H. Huson, R. Rupp, V. Berry, P. Gambette and C. Paul - Computing galled networks from real data, Bioinformatics 2009 25(12):i85-i93; doi:10.1093/bioinformatics/btp217.

If you have any comments or questions then please write us an email. You can also reach this site via: http://www.dendroscope.org

http://www-ab.informatik.uni-tuebingen.de/software/dendroscope
« Last Edit: March 26, 2014, 09:39:54 PM by Software Santa »