It has already been shown that iterative alignment strategies generally perform better than progressive approaches on protein alignments [10]. The same is true for RNA alignments: with increasing number of sequences and decreasing sequence homology iterative programs perform relatively better compared to non-iterative approaches. Figure 2 demonstrates this for PRRN – a representative for an iterative alignment approach – and CLUSTALW as the standard progressive, non-iterative alignment program. The effect is again most notable in the low sequence identity range (APSI < 0.55). In this range, alignment errors occur that can be corrected during the refinement stage of iterative programs. The same can be demonstrated for other iterative vs. non-iterative program combinations like MAFFT or MUSCLE vs. POA or PROALIGN etc. (see supplementary plots on our website [32]).