### Online servers dedicated to graph analysis

**tYNA**: a web tool for managing, comparing and mining multiple networks**DVD**: DVD is a tool for the visualization of the dynamics of multi-state discrete models of biological networks.**CABiNet**: CABiNeT offers a set of methods for network statistics, integration, analysis and clustering.### Visualization / treatment tools

**yED**: yEd is a very powerful graph editor that is written entirely in the Java programming language.**Cytoscape**: Cytoscape is an open source bioinformatics software platform for visualizing molecular interaction networks.**BioEdge plugins for Cytoscape**: Plugins for the analysis of metabolic networks using several graph analysis tools such as k-shortest paths, k-walks, context extraction...**VisANT**: VisANT is a three-tier enterprise system designed specifically for the integrative visual data-mining of multi-scale Bio-Network/Pathways.**JNets**: JNets is a network visualization and analysis tool.**Biological networks**: BiologicalNetworks is a bioinformatics and systems biology software platform for visualizing molecular interaction networks, sequence and 3D structure information.**ProteoLens**: ProteoLens is a next-generation biological network visual data exploration, annotation, and mining tool.**ONDEX**: ONDEX enables data from diverse biological data sets to be linked, integrated and visualised through graph analysis techniques.**Pajek**: Pajek is a freely available general purpose graph visualization and analysis program able to cope with large networks.**Osprey**: Osprey is a software platform for visualization of complex interaction networks.**Network Workbench**: Network Workbench is a large-scale network analysis, modeling and visualization toolkit for biomedical, social science and physics research.**Biological Network Analysis**: C++ and Perl programs useful for studying biological networks### Graph libraries

**JUNG**: JUNG, the Java Universal Network/Graph Framework--is a software library that provides a common and extendible language for the modeling, analysis, and visualization of data that can be represented as a graph or network.**JGraphT**: JGraphT is a free Java graph library that provides mathematical graph-theory objects and algorithms.**Boost**: A standardized generic interface for traversing graphs is of utmost importance to encourage reuse of graph algorithms and data structures.**eXpanda**: eXpanda is provided as a Perl library which gives full-automatic connections to various biological databases via a Perl programmable interface and can perform topological analysis based on graph theory.### Graph based clustering tools

**MCL**: a fast and scalable unsupervised cluster algorithm for graphs based on simulation of (stochastic) flow in graphs (developped by Stijn van Dongen).**MCODE**: a relatively fast method of clustering, although it does not currently provide any statistical score on the resulting clusters. It can be used as discovery tool when analyzing a network (developped by Bader GD and Hogue CW).### Network databases

**KEGG PATHWAY**: KEGG PATHWAY is a collection of metabolic and signal transduction pathway maps.**BioCyc**: BioCyc is a collection of 371 Pathway/Genome Databases that provides reference sources on pathways and genomes of different organisms.**BioGRID**: BioGRID is a repository for interaction datasets.**STRING**: STRING is a database of known and predicted protein-protein interactions.**MIPS**: MIPS provides manually curated genome and interaction databases for several organisms.