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

BioLayout Express 3D

http://www.biolayout.org/

Facilitates microarray data analysis

[89]

Cytoscape

http://www.cytoscape.org/

Versatile; implements many visualisation algorithms; many plug-ins available

[55]

Large Graph Layout (LGL)

http://sourceforge.net/projects/lgl

Especially useful for dynamic visualisation of large graphs (10⁵ nodes, 10⁶ edges); force-directed layout algorithm

[90]

Osprey

http://biodata.mshri.on.ca/osprey/servlet/Index

Provides network filters, connectivity filters, many layouts and facilitates dataset superimposing

[91]

Pajek

http://vlado.fmf.uni-lj.si/pub/networks/pajek/

Especially useful for the analysis of very large networks

[92]

Visant

http://visant.bu.edu/

Especially facilitates analysis of gene ontologies

[53]

Yed

http://www.yworks.com/products/yed/

General purpose graph editor

-