The Cartwheel Bioinformatics Toolkit

See the Cartwheel user site and the FamilyJewels user site for user-friendly documentation.

All of the Cartwheel and FamilyJewels source stuff has been moved from the two SourceForge sites ( and into a single Subversion repository. All of the "active" projects are now available under /trunk/, e.g. /trunk/FRII contains the active development code for FamilyRelationsII.

You can check out individual modules like this:

svn co FRII

Developers can use ssh:

svn co svn+ssh://<user> FRII

You're probably interested in one or more of the following modules: FRII, cartwheel-server, motility, or paircomp.

Contact Titus Brown at if you need check-in access or you would like an account to submit tickets, edit documentation on this Wiki, etc.

Mailing Lists

Announcements of new features and new releases will be made to the cartwheel-announce list.

The cartwheel list is the place for discussion.

If you are interested in ongoing development, the Cartwheel subversion announcements list reports all check-ins. (Subscribe to this if you're actively interested in the Cartwheel source code!)


There is documentation for most of the individual packages under the doc/ subdirectories, e.g. FRII/doc or cartwheel-server/doc.

Adding a BLAST Database to Cartwheel

Generating a pairwise comparison on the command line

Adding a control to the paircomp/seqcomp mapping display controls

Running the Cartwheel Web server with FastCGI

Command line utilities for the Cartwheel server

Using the XML-RPC API for the Web server

Building the Software

Here's a page on BuildingFamilyRelations. If you want to build paircomp or motility independently, just run cmake . && make in the paircomp/ or motility/ subdirectory.

Developers with check-in privileges might check the Cartwheel buildbot page.


Mussa Trac Page