Comparing two models with thousands of reactions is a big problem if models do not come from the same lab or are created using different standards. ModeRator can help here.
ModeRator - The Model Comparator can give insight into the similarity of two models where entities' external identifiers, like, KEGG ID and ChEBI ID are not included.
Metabolites are compared using their names that are available in the model file. Chemical formulas, if available, are used to strengthen or weaken automatic decision about the equality of metabolites. Formulas with different charge can be tolerated.
Reactions are compared based on their metabolites and stoichiometry. Balanced and imbalanced reactions can be compared through tolerance of missing reactants. Models in SBML and COBRA spreadsheet format are supported.
Mednis, M., Brusbardis, V., Galvanauskas, V. (2012) Comparison of genome-scale reconstructions using ModeRator. In Proceedings of IEEE 13th International Symposium on Computational Intelligence and Informatics, Budapest, Hungary, November 20–22, 2012. INSPEC Accession Number: 13446376, 79–84. https://doi.org/10.1109/CINTI.2012.6496737.
Mednis, M., Aurich, M.K., (2012) Application of string similarity ratio and edit distance in automatic metabolite reconciliation comparing reconstructions and models. Biosystems and Information technology, 1(1), pp. 14–18. View full text.