  This document compares SRI's Pathway Tools (PTools) software with the
Reactome software. Both software systems serve the pathway bioinformatics area,
including representation and analysis of metabolic pathways and signaling
pathways. The comparison covers pathway bioinformatics capabilities, but does
not cover other major facets of Pathway Tools that are completely absent from
the Reactome software: Pathway Tools genome-informatics capabilities,
regulatory informatics capabilities, and table-based analysis tools
(SmartTables).
  Our overall findings are as follows. (1) PTools is significantly ahead of
Reactome in its basic information pages. For example, PTools pathway layout
algorithms have been developed to an advanced state over several decades,
whereas Reactome pathway layouts are illegible, omit important information, and
are created manually and therefore cannot scale to thousands of genomes. (2)
PTools is far ahead of Reactome in omics analysis. PTools includes all of the
omics-analysis methods that Reactome provides, and includes multiple methods
that Reactome lacks. (3) PTools contains a metabolic route search tool
(searching for paths through the metabolic network), which Reactome lacks. (4)
PTools is significantly ahead of Reactome in inference of metabolic pathways
from genome information to create new metabolic databases. (5) PTools has an
extensive complement of metabolic-modeling tools whereas Reactome has none. (6)
PTools is more scalable than Reactome, handling 18,000 genomes versus 90
genomes for Reactome. (7) PTools has a larger user base than Reactome. PTools
powers 17 websites versus two for Reactome. PTools has been licensed by 10,800
users (Reactome licensed user count is unknown).
