The influence of the set size on the accuracy and on the running time. We randomly selected sets of 2–10, 12, 14, 16, 18, 20 sequences from each family. Top: The run-time of the algorithm is roughly linear in the number of sequences. Note that although the Sum-of-Pairs stage is quadratic in the number of sequences, it has only a minor effect on the overall run-time. Bottom: The performance of RNAspa (in terms of the MCC) generally improves as the set size increases from two to about seven or eight. Increasing the size of the sets further, does not improve the performance.