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.