Skip to main content

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 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 -