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Multiple alignment (TREEWISE)

Given the initial set of superimpositions, and a set of PAIRWISE similarity scores, the TREEWISE option will perform all alignments that are possible given a dendrogram generated by considering the PAIRWISE scores. Statistics, transformations and alignments are output at each stage of the hierarchy so that a continuum of structure variation can be observed (i.e. the output will become more and more structurally varied as the search progresses).

Note that by default, STAMP performs both PAIRWISE and TREEWISE procedures together.