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Table 2 Examples of tools useful for the visualisation of networks and PPIs.

From: Construction and analysis of protein–protein interaction networks

Tool URL Features Refs.
BioLayout Express 3D Facilitates microarray data analysis [89]
Cytoscape Versatile; implements many visualisation algorithms; many plug-ins available [55]
Large Graph Layout (LGL) Especially useful for dynamic visualisation of large graphs (105 nodes, 106 edges); force-directed layout algorithm [90]
Osprey Provides network filters, connectivity filters, many layouts and facilitates dataset superimposing [91]
Pajek Especially useful for the analysis of very large networks [92]
Visant Especially facilitates analysis of gene ontologies [53]
Yed General purpose graph editor -