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Pathway Tools Features

Comprehensive List of Features in the Pathway Tools Software Suite

See our Pathway Tools overview publication for a comprehensive overview of the software.

  • Modes of Operation
    • Desktop mode (Windows, Mac, Linux)
    • Web mode (Mac, Linux)
  • Genome Informatics
    • Gene/protein/RNA searches
    • Gene information page
    • Circular and linear genome browsers
    • BLAST search
    • Sequence pattern search
    • Multiple sequence alignment
    • Sequence retrieval
  • Pathway Informatics
    • Reaction, metabolite, and pathway searches
    • Reaction, metabolite, and pathway information pages
    • Single pathway diagrams
    • Multi-pathway diagrams
    • Zoomable metabolic network diagrams
    • Pathway inference from annotated genome
    • Quantitative metabolic modeling via flux balance analysis: FBA, dFBA, FVA, gap filling, blocked metabolites
    • Pathway-based inference of nutrient requirements
    • Metabolic route search for metabolic engineering
    • Metabolic route search for microbial communities
    • Metabolic network explorer
  • Regulatory Informatics
    • Operon inference from genome
    • Capture/visualize promoters, transcription factor binding sites
    • Visualize regulon of transcription factor
    • Regulatory network viewer
  • Transcriptomics Data Analysis
    • Enrichment analysis
    • Paint transcriptomics data onto single pathways, zoomable metabolic network
    • Paint transcriptomics data onto regulatory network
    • Paint transcriptomics data onto genome diagram
    • Omics Dashboard
    • Sort pathways by pathway activation score
    • Multi-omics Explainer
  • Metabolomics Data Analysis
    • Enrichment analysis
    • Paint metabolomics data onto single pathways, zoomable metabolic netwok
    • Omics Dashboard
    • Sort pathways by pathway activation score
    • Pathway covering analysis
  • Comparative Analysis
    • Comparative genome browser
    • Compare reaction complements across multiple organisms
    • Compare pathway complements across multiple organisms
    • Compare metabolite complements across multiple organisms
  • Advanced Data Manipulation
    • SmartTables
    • Interactive editing tools
    • Advanced Query Interface
  • APIs:
    • Web services, Python, Java, Perl, R, Lisp
    • Import/Export: SBML, GenBank, GFF, BioPAX, tab-delimited files