MCODE Cytoscape App 2.0

MCODE is a Cytoscape app that finds clusters (highly interconnected regions) in a network. Clusters mean different things in different types of networks. For instance, clusters in a protein-protein interaction network are often protein complexes and parts of pathways, while clusters in a protein similarity network represent protein families. Cytoscape is freely available network visualization and analysis software.

MCODE is a relatively fast method of clustering. With an intuitive interface, it is suited for both computationally and biologically oriented researchers. Current features include:

  • Fast network clustering

  • Fine-tuning of results with numerous node-scoring and cluster-finding parameters

  • Interactive cluster boundary and content exploration

  • Multiple result set management

  • Cluster sub-network creation and plain text export

Currently, MCODE does not provide any statistical score on the resulting clusters but can be used as a discovery tool in network analysis. Please see the MCODE paper for more information.

Feature Requests and Reporting Bugs

The MCODE GitHub issue tracker can be used to report a bug or request a feature.

To Report a bug:

  • Go to

  • Click on New Issue

  • Write a short description of the issue. It is very helpful to provide a series of steps that can be taken to reproduce the issue.

  • If possible attach a session file (.cys) or example input files.

  • Enter App version, Cytoscape version and operating system.

  • Click on Submit new issue