Boxplots of the averaged Cline scores for the 264 alignments of the DNA SMART dataset. The boxplots corresponding to the Cline scores for the DNA SMART dataset are given in this figure. The figures, correspond, from left to right, to the averaged performance of [ClustalW – Ref. ClustalW], [ClustalO – Ref. ClustalO], [Kalign – Ref. Kalign], [Mafft (FFTnsi) – Ref. Mafft (FFTnsi)], [Mafft (Linsi) – Ref.Mafft (Linsi)], [Muscle – Ref. Muscle], [DialignTX- Ref. DialignTX], [GramAlign – Ref. GramAlign], [ProbConsRNA – Ref. ProbConsRNA] and [PicXAA – Ref. PicXAA]. The bars at the bottom of each pair represent the percentage of times where the reformed alignments were superior (blue bars), equal (green bars) or inferior (red bars) in terms of Cline score compared to the initial alignments.