
Name/platform  Description  Type  Webpage 

Cytoscape  An open source software platform for analyzing and visualizing complex networks: integrating a lot of plugins (Apps) concerning network analysis, communication scripting, and functional enrichment for biological network analysis. In addition, the package allows thirdparty developers to extend functionality of network analysis based on Java script [22, 23].  Free  http://www.cytoscape.org/ 

Pajek  A particularly useful package for the analysis of very large networks: integrating many network analysis methods. Thanks to its specific.net data file type, most of the algorithms of network analysis run quickly and scale well [167].  Free  http://pajek.imfm.si/doku.php 

NetworkX  A Pythonbased package for comprehensive analysis of complex networks: integrating many network analysis methods including network structure and analysis measures.  Free  http://networkx.github.io/ 

Ucinet  A comprehensive package for the analysis of network: providing many network analysis methods as well as multivariate statistics. In addition, the package has strong matrix analysis such as matrix algebra and can be used to analyze different mode network data.  Commercial use  http://www.analytictech.com/ucinet/ 

NetMiner  An application software for exploratory analysis and visualization of large network data: providing 73 kinds of network analysis modules, 25 kinds of statistic and mining analysis modules, 28 kinds of visualization algorithms, 21 kinds of data transform modules.  Commercial use  http://www.netminer.com/ 

Guess  An exploratory data analysis and visualization tool for graphs and networks supporting Python which facilitate to the researcher working on graph structures in their own manners.  Free  http://graphexploration.cond.org/ 

Complex Networks Package for Matlab  Providing a comprehensive framework for both static and dynamic network analysis in Matlab.  Free  http://www.levmuchnik.net/Content/Networks/ComplexNetworksPackage.html 

QuACN  An R Package for analyzing complex biological networks: providing function of analysis, classification and comparison for networks by different topological network descriptors [168, 169].  Free  http://cran.rproject.org/web/packages/QuACN/ 
