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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# +