Zmasek bosc2010 aptx

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Zmasek bosc2010 aptx

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

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