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Biological pathway

Pathway Tools is a comprehensive systems biology software system that is associated with the BioCyc database collection.

4 components

  • PathoLogic: Creates a new Pathway/Genome Database (PGDB) containing the predicted metabolic pathways and operons of an organism, given a Genbank or GFF file as input.
  • Pathway/Genome Navigator: Supports query, visualization, and analysis of PGDBs, including omics data analyses. The Navigator powers the BioCyc web site at
  • MetaFlux: Supports development of metabolic flux models.
  • Pathway/Genome Editors: Provide interactive editing capabilities for PGDBs.

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