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  • 1. Evolutionary tree visualization and analysis with Archaeopteryx
    Christian M Zmasek
    Sanford-Burnham Medical Research Institute, La Jolla, California, USA
  • 2. Background
    • Archaeopteryx is a tool for evolutionary tree visualization and analysis
    • 3. Archaeopteryx is based on ATV which was developed to display evolutionary trees with:
    • 4. gene duplications
    • 5. branch length values and support values
    • 6. separate sequence and species names
    Evolutionary tree visualization and analysis with Archaeopteryx
  • 7. Implementation and Availability
    • pure Java(requires Java 1.5 or greater)
    • 8. can be used both as:
    • 9. stand alone application
    • 10. Java Applet (with typical Applet restrictions)
    • 11. Built using/part of the open source foresterframework:
    • 12. http://www.phylosoft.org/forester/
    • 13. forester contains numerous classes for tree IO, tree analysis, etc.
    • 14. Website: http://www.phylosoft.org/archaeopteryx
    • 15. Source code: http://sourceforge.net/projects/forester-atv/
    Evolutionary tree visualization and analysis with Archaeopteryx
  • 16. Some notable features (1/2)
    • phyloXML (http://www.phyloxml.org) support:
    • 17. input
    • 18. output
    • 19. display and editing of most phyloXML elements
    • 20. Support of numerous other formats: Newick, Nexus, Tree of Life XML format, NHX
    • 21. Direct access to a variety of online databases:
    • 22. TreeBASE
    • 23. TreeFam
    • 24. Pfam
    Evolutionary tree visualization and analysis with Archaeopteryx
  • 25. Some notable features (2/2)
    • Display of large trees (>20,000 nodes)
    • 26. Zoom and interactive overview
    • 27. Built in tools and algorithms for analysis:
    • 28. Duplication inference
    • 29. Inference of ancestral taxonomies using UniProt database
    • 30. Tree level editing (cut, copy, paste, re-root, …)
    Evolutionary tree visualization and analysis with Archaeopteryx
  • 31.
  • 32. Biological study example
    Evolutionary tree visualization and analysis with Archaeopteryx
    Example of analysis performed using forester/phyloXML/Archaeopteryx:
    Zmasek CM, Zhang Q, and Godzik A:
    “Analysis of functional profiles of eukaryotic genomes reveals strong trends related to morphological complexity”
    Late Breaking Research LBR21
    Tuesday, July 13: 14:15 - 14:40
  • 33. Evolutionary tree visualization and analysis with Archaeopteryx
    http://www.phylosoft.org/archaeopteryx