Comprehensive List of Features in the Pathway Tools Software Suite

• 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