Gephi is the canonical answer for visualization but it can also compute some graph theoretic measures and use it for coloring, sizing etc.  

From a tutorial by Paola Tubaro & Yasaman Sarabi:

R packages: SNA, tnet, PNet, RSiena.

*SNA, tnet: metrics, basic models and visualisation;

*PNet for ERGM (cross-section modeling);

*RSiena for longitudinal data modeling (SAOM);

*More difficult at the beginning, but more powerful and versatile; Freely available.

UCINET and Netdraw

*For data management, metrics, basic models, and visualisation.

*Easy to use, widely used; Comprehensive tutorial available on the web, good Help function; Free for one-month trial, then needs to be purchased.

Pajek

*For exploratory data analysis and visualisation; Good for large networks, widely used; Some tutorials available on the web, a support book; Freely available online.

Assalam o Alikumn, You can use R, Rapidminer for it!

Gephi is the canonical answer for visualization but it can also compute some graph theoretic measures and use it for coloring, sizing etc.  

From a tutorial by Paola Tubaro & Yasaman Sarabi:

R packages: SNA, tnet, PNet, RSiena.

*SNA, tnet: metrics, basic models and visualisation;

*PNet for ERGM (cross-section modeling);

*RSiena for longitudinal data modeling (SAOM);

*More difficult at the beginning, but more powerful and versatile; Freely available.

UCINET and Netdraw

*For data management, metrics, basic models, and visualisation.

*Easy to use, widely used; Comprehensive tutorial available on the web, good Help function; Free for one-month trial, then needs to be purchased.

Pajek

*For exploratory data analysis and visualisation; Good for large networks, widely used; Some tutorials available on the web, a support book; Freely available online.

I agree: Gephi is the best... Take care of the operative system that you have in you PC or MAC. With the last version of the OS for Mac, i have some problems in working with Gephi. But the output are really very good.. less from the point of view of the statistical analysis. But you can use Ucinet for this. 

KeyLines, although currently they do not offer academic licenses.

Thanks to all of you for answers.

Try Tapad here: http://www.tapad.com 

You might also want to check out Astute. I've used that before. Works, but you may have to pay to access it. 

All the best with your project!

try head/tail breaks: http://en.wikipedia.org/wiki/Head/tail_Breaks

Jiang B. (2015), Head/tail breaks for visualization of city structure and dynamics, Cities, 43, 69-77, Preprint: http://arxiv.org/ftp/arxiv/papers/1501/1501.03046.pdf

Jiang B. and Miao Y. (2014), The evolution of natural cities from the perspective of location-based social media, The Professional Geographer, xx(xx), xx-xx, DOI: 10.1080/00330124.2014.968886,  Preprint: http://arxiv.org/abs/1401.6756

Jiang B., Duan Y., Lu F., Yang T. and Zhao J. (2014), Topological structure of urban street networks from the perspective of degree correlations, Environment and Planning B: Planning and Design, 41(5), 813-828.

Also, Try Pajek...

I think -JupyteR is an open-source project enabling Big Data analysis, visualization and real-time collaboration on software development across more than a dozen of programming languages. The interface holds the field for code input, and the tool runs the code to deliver the visually-readable image based on the visualization technique chosen.