Comparison of performance of DEDAL and DALI on SISYPHUS alignments. The quality with which the SISYPHUS alignments are reproduced by DEDAL (blue) and DALI (DaliLite, red) on the (a) SCOP, (b) MD (multi-domain), and (c) MC (multi-chain) subsets of the dataset (see text for description), presented as box-and-whisker distribution plots of the agreement with the reference alignments. Each entry corresponds to a set of pairwise comparisons carried out for each of the SISYPHUS multi-alignments. The entries are ordered by the performance of DALI (on SCOP and MD sets), or DEDAL (on the MC set). Box-and-whisker plots represent lower and upper quartiles (box) relative to the median (horizontal line) of the results obtained for a given SISYPHUS multi-alignment, as well as minimum and maximum values (whiskers). When a distribution is reduced to the alignment of a single pair of structures the box-and-whisker plots are correspondingly reduced to a single value. Asterisks indicate alignments containing segment swaps, or circular permutations. For numerical results see Additional files 5, 6 and 7. While DALI performs slightly better than DEDAL on the easier cases (left-hand-side of the SCOP set), DEDAL does better on more difficult and multi-domain alignments (DALI does not align multi-chain proteins).