Graph Databases (Neo4J)

Neo4j is an open-source graph database, implemented in Java. The developers describe Neo4j as “embedded, disk-based, fully transactional Java persistence engine that stores data structured in graphs rather than in tables”. Neo4j is the most popular graph database. [source: https://en.wikipedia.org/wiki/Neo4j]
http://neo4j.com/

Gephi is an open-source network analysis and visualization software package written in Java on the NetBeans platform, initially developed by students of the The University of Technology of Compiègne (Université de Technologie de Compiègne or UTC) in France. Gephi has been selected for the Google Summer of Code in 2009, 2010, 2011, 2012, and 2013.  Gephi has been used in a number of research projects in the university, journalism and elsewhere, for instance in visualizing the global connectivity of New York Times content and examining Twitter network traffic during social unrest along with more traditional network analysis topics. [source: https://en.wikipedia.org/wiki/Gephi]
http://gephi.github.io/

Graphviz is open source graph visualization software. Graph visualization is a way of representing structural information as diagrams of abstract graphs and networks. It has important applications in networking, bioinformatics,  software engineering, database and web design, machine learning, and in visual interfaces for other technical domains.  [source: http://www.graphviz.org/]
http://www.graphviz.org/