MicrobiomeNet offeres both the standard Jaccard Index as well as weighted Jaccard Index for comparing the two pathways. The weighted Jaccard index incorporates reaction abundance (i.e. the frequency of those reactions within that pathway). The weighted Jaccard Index accounts for the “dosage” or “compositional weight” of each reaction rather than just its presence.
If Pathway 1 has 10 copies of Reaction A and Pathway 2 has only 1 copy, the Weighted Jaccard will reflect this “imbalance.” It recognizes that while the type of reaction is shared, the capacity of that reaction within the pathway is fundamentally different. Low weighted Jaccard indices (often below 0.15 and occasionally <0.05) suggest not only limited reaction overlap but also strongly divergent reaction-frequency patterns (i.e. more likely to be complementary)