1. Evolutionary tree visualization and analysis with Archaeopteryx Christian M Zmasek Sanford-Burnham Medical Research Institute, La Jolla, California, USA

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 namesEvolutionary tree visualization and analysis with Archaeopteryx

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

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. PfamEvolutionary tree visualization and analysis with Archaeopteryx

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

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