Running time of Mumsa in comparison to the alignment methods used as input. The running time in CPU seconds for Mumsa using three settings in comparison to the cumulative running time of the alignment programs used to generate the input alignments. The running times of Mumsa were multiplied by 100 to be visible in the plot. The sequence files were generated by ROSE  using an average sequence length of 500 residues and and average evolutionary distance of 250. It is clear that the running time of Mumsa is at least two orders of magnitude lower than that required by the alignment programs.