Table 1.

Empirical evaluation of our top four interactive network visualization tools (Cytoscape, Gephi, Tulip, and Pajek) for large-scale biological network analysis.

	Cytoscape	Tulip	Gephi	Pajek
Scalability	∗∗	∗	∗∗∗	∗∗∗∗
User friendliness	∗∗	∗∗∗∗	∗∗∗	∗
Visual styles	∗∗∗∗	∗∗	∗∗∗	∗
Edge bundling	∗∗∗	∗∗∗∗	∗∗	—
Relevance to biology	∗∗∗∗	∗∗	∗∗∗	∗
Memory efficiency	∗	∗∗	∗∗∗	∗∗∗∗
Clustering	∗∗∗∗	∗∗∗	∗	∗∗
Manual node/edge editing	∗∗∗	∗∗∗∗	∗∗∗	∗
Layouts	∗∗∗	∗∗	∗∗∗∗	∗
Network profiling	∗∗∗∗	∗∗	∗∗∗	∗
File formats	∗∗	∗∗∗	∗∗∗∗	∗
Plugins	∗∗∗∗	∗∗	∗∗∗	∗
Stability	∗∗∗	∗	∗∗∗∗	∗∗∗
Speed	∗∗	∗	∗∗∗	∗∗∗∗
Documentation	∗∗∗∗	∗	∗∗	∗∗∗

∗ = weaker; ∗∗ = medium; ∗∗∗ = good; ∗∗∗∗ = strongest.