Pairwise comparisons and alignments (PAIRWISE)

Given a suitable initial superimposition of structures, the best way to obtain a multiple alignment and superimposition of a diverse family of domains is to follow a hierarchy of similarity. This allows most similar domains to be compared/aligned first, and only makes comparisons/alignments between distantly related domains at a later time in the procedure.

Pairwise comparisons are an ideal way to obtain such a hierarchy. The PAIRWISE options in STAMP will result in all $N \times (N-1)/2$ comparisons being performed and will output a matrix of pairwise similarities. This can then be used to produce a dendrogram, or tree, from which multiple alignments and superimpositions may be generated.