Pathway Tools

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The Pathway Tools software is a bioinformatics software system for pathway analysis of genomes, and for creating Pathway/Genome Databases (PGDBs). A pathway/genome database (PGDB), such as EcoCyc, is a bioinformatics DB that integrates genomic data with detailed functional annotations of the genome, such as descriptions of metabolic and signaling pathways. A PGDB is a type of model-organism DB.

Pathway Tools supports extensive functionality including prediction, interactive editing, querying, and visualization of metabolic pathways and related datatypes including reactions, metabolites, and enzymes. It also includes query, visualization, and editing support for operons, genes, proteins, and chromosomes.

Pathway Tools can be coupled with other genome browsers to add support for pathways to an existing MOD.

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

Demo & Screenshots
See Samples
Sun workstation, Windows2000 or XP, or Linux.
See the Pathway Tools Information Site for links.
Facts about "Pathway Tools"RDF feed
Available on platformweb +, linux +, os x + and windows +
Date published2010 +, 2011 + and 2012 +
Has DOI10.1093/bib/bbp043 +, 10.1093/database/baq006 +, 10.4056/sigs.1794338 + and 10.1186/1471-2105-13-243 +
Has PMCIDPMC2810111 +, PMC2911841 +, PMC3368424 + and PMC3473263 +
Has PMID19955237 +, 20624715 +, 22675592 + and 22998532 +
Has URL +, +, +, + and +
Has authorKarp PD +, Paley SM +, Krummenacker M +, Latendresse M +, Dale JM +, Lee TJ +, Kaipa P +, Gilham F +, Spaulding A +, Popescu L +, Altman T +, Paulsen I +, Keseler IM + and Caspi R +
Has descriptionlist of PGDBs hosted elsewhere + and Pathway Tools is a comprehensive symbolic Pathway Tools is a comprehensive symbolic systems biology software system that supports several use cases in bioinformatics and systems biology:
  • Development of organism-specific databases called Pathway/Genome Databases (PGDBs) that integrate many bioinformatics datatypes, from genomes to pathways to regulatory networks.
  • Development of metabolic-flux models using flux-balance analysis
  • Scientific visualization, web publishing, and dissemination of those organism-specific databases, including:
    • Automatic display of metabolic pathways and full metabolic networks; generation of metabolic map diagram and of metabolic map poster (example).
    • Genome browser; comparative genome browser; generation of genome poster (example).
    • Display of operons, regulons, and full transcriptional regulatory networks
  • Analysis of omics datasets, including painting omics data on to diagrams of the full metabolic network, enrichment analysis.
  • Computational inferences including prediction of metabolic pathways, prediction of metabolic pathway hole fillers, prediction of operons
  • Comparative analyses of model-organism databases.
  • Analysis of biological networks:
    • Interactively tracing metabolites through the metabolic network
    • Finding dead-end metabolites in metabolic networks
    • Identifying choke points (potential drug targets) in metabolic networks

Pathway Tools has four components:

  • PathoLogic: Creates a new PGDB containing the predicted metabolic pathways of an organism, given a Genbank entry as input.
  • Pathway/Genome Navigator: Supports query, visualization, and analysis of PGDBs. The Navigator powers the BioCyc web site at
  • MetaFlux: Supports development of metabolic flux models from Pathway/Genome Databases.
  • Pathway/Genome Editors: Provide interactive editing capabilities for PGDBs.nteractive editing capabilities for PGDBs. +
Has development statusactive +
Has download URL +
Has input formatGenbank format + and GFF +
Has logoPathwayTools.png +
Has output formatGenbank format +, SBML + and BioPAX +
Has publication detailsBriefings in bioinformatics 11: 40-79 +, Database : the journal of biological databases and curation 2010: baq006 +, Standards in genomic sciences 5: 424-9 + and BMC bioinformatics 13: 243 +
Has software maturity statusmature +
Has support statusactive +
Has titlePathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology. +, An advanced web query interface for biological databases. +, The pathway tools pathway prediction algorithm. +, Regulatory network operations in the Pathway Tools software. +, E. coli PGDB + and Other PGDBs +
Has topicPathway Tools +
Has website +
Is open sourceCaveats apply +
Link typedownload +, website +, public server + and wild URL +
Published inBriefings in bioinformatics +, Database : the journal of biological databases and curation +, Standards in genomic sciences + and BMC bioinformatics +
Release date1999 +
Tool functionality or classificationCommunity Annotation +, Comparative Genome Visualization +, Database schema +, Database tools +, Gene Expression Visualization +, Genome Visualization & Editing +, Molecular Pathway Visualization + and Ontology Visualization +
Has subobjectThis property is a special property in this wiki.Pathway Tools# +, Pathway Tools# +, Pathway Tools# +, Pathway Tools# + and Pathway Tools# +