Cytoscape plugins

• NetworkEvolution plugin provides the capability to visualize censecutive evolutionary stages of protein interaction networks based on phylogenetic information.
• APCluster plugin implements a recent Affinity Propagation algorithm for graph clustering.

The source code can be downloaded from http://code.google.com/p/misiek/.
All implemented software is open source (GPL 3.0 license).

Requirements

• Cytoscape 2.6.3 or later (http://www.cytoscape.org/)
• Java 1.6
• Tested on Cytoscape 2.6.3 on Windows, Linux and Mac OS.

Data

The exemplary input files are provided below. The format of the data is described in the manual.

• Species tree
• Protein family trees
• Interactions
• Experiments
• Interactions (multiple files)