CRIMSON
| Maintained by Stephen Fisher | License (pdf) |
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.
Crimson was created as part of
the Cyberinfrastructure for
Phylogenetic Research (CIPRES) project. 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.