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.