Time complexity for RSE. The number of refinement cycles and the CPU time per refinement cycle were recorded for each of the 3,591 CDD alignments. Panel (A) gives the histogram of the number of alignments vs. the number of refinement cycles. There is no alignment with one cycle because RSE always executes one additional final cycle (unless no alignment is found in the first cycle). Panel (B) gives the CPU times per cycle as a function of the size of the alignment matrix.