Modeling

The CRIMSON database is now available for testing.

For more information, contact Stephen Fisher

Crimson facilitates the extraction of sub-trees from very large phylogenetic trees. Trees are loaded into a shared database, and sampled according to schemes controlled by the user. Comprehensive graphical dialogs allow users to easily manage and query trees in the database. Queries can be stored in the database to be shared with other users and moved between databases. A command line interface enables users to write their own function and scripts to manager the database, manipulate the trees and queries, and automate any of the built-in functions.

This application has been tested on Windows and Linux systems and should run on any system that contains Java 1.5 or later. Both Oracle and MySQL databases can be used.

To access the CIPRES database, open an Oracle database connection using 'http://cipres.sdsc.edu/DatabaseProxy.php' as the server, with a blank username and password. From the Crimson command line, this can be done using the following command:

  >>> openDatabase("","", "http://cipres.sdsc.edu/DatabaseProxy.php")

This web proxy allows for read-only access to the CIPRES database. Contact Mark Miller at SDSC to gain write access to this database.

Screen shots...

Download:

• Executable (Windows, Linux, Mac OS X - Mar 3, 2008)
• Sample data (45 MB zipped file)
• Documentation (pdf)
• API Documentation (html)

CIPRES is a Collaboration of the Following Institutions:
American Museum of Natural History, Florida State University, New Jersey Institute of Technology, North Carolina State University, Rice University, San Diego Supercomputer Center, Texas A&M, University of Arizona, University of British Columbia, University of California at Berkeley, University of California at San Diego, University of Connecticut, University of Pennsylvania, Univ. of South Carolina, University of Texas at Austin, and Yale University. xhtml | css