MCODE is an extension for Cytoscape and can only be accessed through Cytoscape:
- Start Cytoscape.
- Import a network or open a Cytoscape session that has one or more networks.
- Make sure a network is selected in Cytoscape's.
- Select the menu option Apps > MCODE, which should open MCODE's New Analysis Dialog.
- Click the Analyze Current Network button.
- The main MCODE interface will appear with the results as a tab in the left-hand panel of Cytoscape.
