Correlations of flux predictions by three methods. Measured values of 31 fluxes from the Tomita data set were compared to predictions using the FBA, MOMA and PSEUDO objective functions. (A) Pearson correlations of flux predictions from the three methods for each of 12 metabolic deletion mutants. (B) Meng's Z-test was applied to the hypothesis that PSEUDO-derived correlation coefficients were higher than those derived using FBA (red circles) or MOMA (blue squares). The dotted line indicates a significance threshold of 0.05. PSEUDO significantly outperformed MOMA in every case and FBA in 9 of 12 cases. Exact correlation coefficients and p-values are reported in Additional file 3: Table S1.