Network analysis and visualization software

• R is a powerful open source statistical computing application. It has easy scripting, visual output, and data analysis. Network analysis is easy with the igraph package (see below).
• Agna is another Java based tool with a nice interface for data entry/editing, and a separate window for visualization and layout.
• Gephi an open-source, cross platform tool for network exploration. Makes beautiful, highly customizable, plots.
• GUESS is a powerful visualization and analysis tool written with Python.
• Tulip is open source and written with Qt/C++/OpenGL and has a lot of interesting, interactive features, not to mention a beautiful logo. The interface is very creative, and documentation is extensive.
• SocNetV is an open-source graph manipulation/visualiation appliation for Linux, built with C++ and Qt (Qt4 package required) with a simple graphical interface. Easy to use, keeps it simple.
• SoNIA is a Social Network Image Animator, and can be used to create interesting layouts, as well as videos of evolving networks.
• NetworkX is an open-source, terminal-based python program with simple commands and lots of features for manipulation and visualization of graphs.
• Network Workbench is a powerful application written in Java with lots of analysis tools, though the interface is not very friendly.
• Pajek (old) is a popular layout and analysis tool that has a lot of good features. It is, however, only for Windows, and is not open source.
• FANMOD is “a tool for fast network motif detection”, multi-platform binaries and source code are available. Has GUI and command-line versions.
• NAViGaTOR is written in JAVA with OpenGL for visualization and analysis of biological networks.
• NetVis is a web-based and open-source tool for network data collection, visualization, and analysis. It is written in PHP and Java.
• yED is a Java-based graph drawing and layout tool with some data anlaysis. Drawings and layout for graphs and diagrams are interactive, and look nice.

Programming libraries

• igraph is a great package for graph manipulation, generation and visualization. Library is written in ANSI C, and works with C/C++, R, Python, and Ruby.
• Boost Graph Library is a powerful library class with lots of flexibility in data structures, and includes pretty much any algorithm you might need.
• Open Graph Drawing Framework is an easy to use, self-contained class library for analysis and layout, written in C++.
• JUNG is a Java-based class library for graph visualization.

Academic journals, research groups, societies

• International Network for Social Network Analysis
• Social Networks
• Journal of Social Structure
• REDES: Revista Hispana para el análisis de Redes Sociales
• Physical Review E
• Journal of Mathematical Sociology

Learning resources

• Graph Theory, a free textbook by Reinhard Diestel. Full online version available in English and German.
• Free textbooks including: Introduction to social network methods and Computer-Assisted Theory Building: Modeling Dynamic Social Systems by Robert Hanneman, and others.
• Dynamics of Complex Systems, a free textbook by Yaneer Bar-Yam.
• Graph theory glossary is a good Wikipedia list of annoted graph theory terminology

Data Sets

• Gephi Data Sets Les Miserables, Zachary’s Karate Club, Github open-source developers, and others in a variety of formats.
• MEJ Newman’s Page College football, dolphins, power grid, collaborations in network science, all GML format
• NetWiki Shared Data Brain, Facebook, MLB hitter-batter matchups, variety of formats

Fun

• Muckety is a news source that investigates the people and connections behind the headlines, and has interactive social network maps of the rich and powerful.