Super
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Overview
super aligns two selections. super is more robust and accurate than align. For syntax, see align.
Algorithm Details
super does a BLAST-like BLOSUM62-weighted dynamic programming sequence alignment followed by a series of refinement cycles intended to improve the fit by eliminating pairing with high relative variability (e.g. >2 standard deviations from the cycle's mean deviance). Next, it does a sequence-independent structure-based dynamic programming alignment followed by that same 3D refinement strategy.