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Table 1 A comparison table of related network visualization tools.

From: Integration of interactive, multi-scale network navigation approach with Cytoscape for functional genomics in the big data era

Tools / Features Cluster Generation Multi-Scale Navigation Purpose of Use Architecture Flexible Navigation Beyond Cluster Boundaries Measures for Handling Insufficient Clustering
NaviClusterCS Automatic and Extremely Fast Yes Generic Cytoscape Plug-in Yes (via Re-centering) Property-Based Clustering
CyOog (Power Graph) [22] Automatic Yes (Power Nodes) Generic Cytoscape Plug-in No No
clusterMaker [15] Automatic Yes (Dendrogram) Generic Cytoscape Plug-in No No
CyClus3D [23] Automatic No Generic Cytoscape Plug-in No No
NeMo [24] Automatic No Generic Cytoscape Plug-in No No
BioLayout Express3D [25] Automatic No Generic Stand-Alone No No
jClust/Medusa [26, 27] Automatic No Generic Stand-Alone No No
MODEVO [16] Automatic No Protein Interaction Network Cytoscape Plug-in No No
RobinViz [17] Automatic No Protein Interaction Network Stand-Alone Yes (2-Hop Neighborhood) No
VisANT [12] Manual Yes (Metanodes) Generic Stand-Alone No No
Cellular Overview [13] Manual and Stored in Databases Yes (Zooming User Interface) Metabolic Network Web-Based No No
GenePro [14] Manual No Interaction Network Cytoscape Plug-in No No