The one-minute guide to using ClusterONE

ClusterONE is distributed in a Java archive file (JAR), which contains both the command line application and the Cytoscape plugin. In this document, we are assuming that you want to use ClusterONE from the Cytoscape graphical user interface. If you are interested in the command line interface, please refer to the documentation distributed with the command line interface itself.

ClusterONE can be installed from the Cytoscape plugin manager. Launch Cytoscape if you have not done so, click on the Manage plugins item of the Plugins menu, select the Analysis subgroup within the Available for install category, select the line starting with ClusterONE and click on the Install button. Cytoscape should download and install the selected version of ClusterONE for you. If you see more than one version of Cluster ONE, make sure you install the most recent one. If you don't see any Cluster ONE version, first check whether you have installed it already (look for a menu called ClusterONE within the Plugins submenu), and if you haven't, check the Show outdated plugins checkbox in the Manage plugins dialog.

If you managed to install ClusterONE successfully, you should see a new menu item called ClusterONE in the Plugins submenu. Now, do the following: