Software applications
[http://www.cytoscape.org Cytoscape] in Java. Freely available (open-source)
Programming Libraries
[http://www.cytoscape.org Cytoscape] in Java. Freely available (open-source)
[https://networkx.lanl.gov/ NetworkX] in Python
[http://sbi.imim.es/piana/ PIANA] in Python.
[http://www.bioconductor.org/packages/bioc/stable/src/contrib/html/graph.html Bioconductor graph package] in R. Freely available (open-source)