Performance comparison of RNAfold 2.0 to other secondary structure prediction software. (A) Accuracy of thermodynamic folding programs in terms of cumulative distribution of the Matthews correlation coefficient (MCC). RNAfold 2.0 outperforms the other secondary structure prediction programs on the RNAstrand dataset: more of its predictions fall into the region of higher performance values. Both versions of RNAfold were run with -d2 option. For UNAFold and RNAStructure default options were used. Performance distributions of Sensitivity, Positive predictive value (PPV) and F-measure are shown in Additional File 1. The averaged overall accuracies can be taken from table 2. (B) Comparison of runtimes for MFE structure predictions. Measurement was performed on an Intel® Core™ 2 6600 CPU running at 2.4 GHz. Shown are averaged running times for random sequences of lengths 100 nt (100 samples), 500 nt (100 samples), 1000 nt (100 samples), 2500 nt (20 samples), 5000 nt (16 samples) and 10000 nt (16 samples). While the compared programs RNAfold 2.0, RNAfold 1.8.5 and UNAfold 3.8 were capable of predicting an MFE structure for all tested samples in a relatively small time frame, RNAstructure 5.2 was omitted from predictions for the 10000 nt sample set due to its time requirements.