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Pathway Tools Overview
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Pathway Tools Software

Pathway Tools Software

Pathway Tools is a comprehensive bioinformatics software package that spans enterprise genome data management, systems biology, and omics data analysis. The software has been licensed by more than 11,000 groups and powers BioCyc.org and a number of other pathway/genome database websites. The software supports the following use cases:

  • Develop organism-specific databases that integrate many bioinformatics datatypes, from genomes to regulatory networks to metabolic and signaling pathways.

  • Computational inferences including metabolic reconstruction and operon prediction.

  • Scientific visualization and dissemination of those organism-specific databases via a public or private website:
    • Multiple search tools
    • Information pages for genes, metabolic pathways, reactions, and metabolites
    • A genome browser, metabolic network browser, and regulatory network browser

  • Analysis suite for gene-expression and metabolomics data.

  • Development of quantitative metabolic models.

  • Comparative genome and pathway analyses.

  • Analysis of biological networks:
    • Search for routes between specified metabolites
    • Find dead-end metabolites
    • Identify choke points (potential drug targets) in metabolic networks

For a comprehensive summary of the Pathway Tools capabilities click here.

More Information

Pathway Tools Licensing

Pathway Tools is freely available to academics for research purposes, and is available for a

Contributions to Pathway Tools

We gratefully acknowledge the following contributions to Pathway Tools:

  • Development of the PerlCyc Perl API to Pathway Tools by Lukas Mueller of Boyce Thompson Institute
  • Development of the JavaCyc Java API to Pathway Tools by the TAIR project
  • Development of the RCyc API for the R Project by Tomer Altman of Stanford University
  • Development of the SBML output module by Jeremy Zucker of the Broad Institute

Pathway Tools User Group Meetings

Additional Information

Contact Us

Pathway Tools was developed by Peter D. Karp and coworkers at the Bioinformatics Research Group at SRI International.

Subscribe to the Pathway Tools Mailing List: Mailing list members receive periodic news and updates about Pathway Tools, such as announcements regarding new releases of the software and databases. The mail volume tends to be less than 1 announcement per month.

To subscribe to the Pathway Tools mailing list, send an email to with the word subscribe in the Subject.

Funding Sources

The development of Pathway Tools is funded by grants GM077678, GM080746, and GM75742 from the National Institutes of Health.


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