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CRIMSON

Subtree extraction from very large phylogenetic trees

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 and a blank username/password. From the Crimson command line, use the 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.

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For information contact:

Stephen Fisher
Department of Biology
University of Pennsylvania
103 Lynch Laboratories
433 S University Ave
Philadelphia, PA 19104
(215) 898-8395
safisher@sas.upenn.edu 		Junhyong Kim
Department of Biology
University of Pennsylvania
103 Lynch Laboratories
433 S University Ave
Philadelphia, PA 19104
(215) 746-5187
junhyong@sas.upenn.edu

logos American Museum of Natural History Florida State University New Jersey Institute of Technology North Carolina State University Rice University San Diego Supercomputer Center State University of New York at Buffalo 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 New Mexico University of Pennsylvania Univ. of South Carolina University of Texas at Austin Yale University

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, State University of New York at Buffalo, 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 New Mexico, University of Pennsylvania, Univ. of South Carolina, University of Texas at Austin, and Yale University.