Pathway Tools pipeline

Pathway Tools specifications


Unique identifier OMICS_03843
Name Pathway Tools
Software type Package/Module
Interface Graphical user interface
Restrictions to use Academic or non-commercial use
Input format PathoLogic, DAT, FBA
Output format FLATFILE
Operating system Unix/Linux, Mac OS, Windows
Computer skills Medium
Version 19.0
Stability Stable
Maintained Yes


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  • person_outline Pathway Tools Team <>

Publications for Pathway Tools

Pathway Tools citations

PMCID: 3372971

[…] using the nj algorithm as implemented in the mega4 package (46). central metabolic pathways were reconstructed using pathway tools version 14 (47). the annotation files required as the input to pathway tools were prepared from the consensus results of two approaches. first, amino acid sequences of predicted proteins were annotated based on their best blast matches against the nr (48), kegg […]

PMCID: 2705386

[…] [19,20]. this suite of analytical tools, linked to a comprehensive interaction and biological function database, is available as a stand-alone application and can be linked via a "plugin" to other pathway tools such as cytoscape [21]. biological networks were built starting from either gene expression data alone, or a combination of high content data sets reflecting multiple levels […]

Pathway Tools institution(s)
Artificial Intelligence Center, SRI International, Menlo Park, CA, USA
Pathway Tools funding source(s)
Supported by grants GM75742, GM080746 and GM077678 from the National Institutes of Health.

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