Boxplots of the averaged Cline scores of the considered alignment pairs for the 2,218 alignments of the BRAliBase dataset. The boxplots of the Cline scores averaged over all 2,218 test cases of the BRAliBase dataset are given at this figure. The figures are organized in pairs corresponding, 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], [PicXAA – Ref. PicXAA], and [RCoffee – Ref. RCoffee]. 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.