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This program allows you to tidy up gaps that are not meaningful in the context of a multiple sequence alignment derived from structure. In other words, regions that are not similar across all members of a structural family can be `cleaned' to remove isolated residues aligned in the middle of nowhere. Note that one doesn't always want to do this (since the sub-alignments can be meaningful). I just find this useful if I am preparing a figure for publication or something.

The format is:

stamp_clean <stamp alignment file> <minimum segment length> > <output file>

The <minimum segment length> is the minimum number of residues that is to be considered significant. I always use 3, since this means that short stretches of 1-2 residues that are surround by gaps (i.e. in any sequence) are `cleaned'. Try it and see what I mean.

Geoff Barton