This program provides input for ALSCRIPT , GJB's program
for the display of multiple sequence alignments. To get a copy of
this program, refer to GJB at the above address.
The format is:
dstamp -f <STAMP alignment file> -prefix <output prefix> (-<parameter> [<value>])
where <parameter> is one of the many parameters described below.
The new command line argument -P reads in parameter files, so if
you have old DSTAMP files, they can still be read in this way.
The parameters for DSTAMP, and their defaults, are (parameter names are case insensitive):
Prefix specify the name of the alscript (.als) and postscript files (.ps) to be generated.
Default prefix = `alscript'
The type of STAMP data to be used (ie. the first letter that occurs after the `#' characters in STAMP multiple alignment output). Default t = `G'
The minimum (or maximum in the case of RMS deviation) value to make a position considered as reliably aligned.
Default c = 6.0
The minimum length of a stetch of reliable regions to be allowed.
Default w = 3
This is the number of sequences that can be ignored during the calculation of residue or residue-property conservation (i.e. if ignore = 1 you allow one `error' in one sequence during the calculation of conserved positions).
Boolean parameter. If specified, the output will be in colour (via alscript).
Boolean parameter. If specified, then a motif is written in the space between the sequence alignment and the aligned secondary structures.
The output is an ALSCRIPT command file.