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.

Screen shots...

Download (9MB zipped file)

Documentation (pdf)

For information contact:

Stephen Fisher Department of Biology University of Pennsylvania 103 Lynch Laboratories 415 S University Ave Philadelphia, PA 19104 (215) 898-8395 safisher@sas.upenn.edu

Junhyong Kim Department of Biology University of Pennsylvania 103 Lynch Laboratories 415 S University Ave Philadelphia, PA 19104 (215) 746-5187 junhyong@sas.upenn.edu

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