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

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... ed 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).