The programs contained within the package

STAMP consists of the main program (usually referred to as STAMP) and several sub-programs. Briefly, the programs are:

STAMP	Main program, does PAIRWISE, tree
	construction, TREEWISE and SCAN modes.
ALIGNFIT	Given a list of domains and a multiple sequence
	alignment outputs an initial transformation.
PDBC	Finds and reports information about PDB files
	given a four (PDB) code and/or chain identifier.
TRANSFORM	Given a list of transformations, outputs the
	corresponding set of coordinates.
SORTTRANS	Sorts the output from SCAN, and removes repeated
	transformations.
PDBSEQ	Given a list of domains, extracts the corresponding
	sequences from the PDB files.
VER2HOR	Given a STAMP alignment file, outputs an easy to read
	text version of the alignment for quick analysis.
DSTAMP	Given a STAMP alignment file, outputs commands for
	GJB's program ALSCRIPT (alignment to Postscript).
GSTAMP	Given a STAMP alignment file, outputs commands for
	Per Kraulis' MOLSCRIPT program.

AVESTRUC	Given a STAMP alignment file, generates an average
	set of main chain or C alpha coordinates for the
	structural family.
POSTSTAMP	Reanalyses a STAMP alignment file (provides a more
	accurate set of equivalences for alignments of more
	than one structure).
PICKFRAME	Given a transformation, transforms all other domains
	onto another (specified by the user).
MERGETRANS	Given two transformation files, merges them by centering
	on a common identifier, either the first common one found
	or one specified by the user.
MERGESTAMP	Given two files containing alignments or transformations or both
	merges them by centering on a common identifier, either the first
	common one found or one specified by the user.
EXTRANS	Given a transformation file and a list of domain identifiers
	it will output a new transformation file containing only the
	domains given
ACONVERT	General alignment format conversion utility.
STAMP_CLEAN	Tidies up STAMP alignments to remove nonsensical gaps