This program provides input for ALSCRIPT [Barton, 1993], 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> (-P <optional parm file> -<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):
TYPE <character> (or -c <character>)
The type of STAMP data to be used (ie. the first letter that
occurs after the `#' characters in STAMP multiple alignment
output).
Default TYPE = `G'
CUTOFF <float> (or -t <float>)
The minimum (or maximum in the case of RMS deviation) value to make
a position considered as reliably aligned.
Default CUTOFF = 6.0
WINDOW <integer> (or -w <integer>)
The minimum length of a stetch of reliable regions to be allowed.
Default WINDOW = 3
SEC <boolean>
If TRUE, then display all secondary structure assignments.
Default SEC = TRUE
SECSUM <boolean>
If TRUE, then display a simple summary of secondary structure
assignments rather than all of them. The `SEC' options below
should apply this summary.
Default SECSUM = FALSE
BOXSEQ <boolean>
If TRUE, then box reliably aligned sequences.
Default BOXSEQ = TRUE
BOXSEC <boolean>
As for BOXSEQ, but for secondary structure assignments.
Default BOXSEC = TRUE
BOLDSEQ <boolean>
If TRUE, then reliably aligned sequence positions will be in
boldface.
Default BOLDSEQ = TRUE
BOLDSEC <boolean>
As for BOLDSEQ, but for secondary structure assignments.
CASESEQ <boolean>
If TRUE, then reliably aligned sequence positions will be in upper
case, unreliably aligned in lower case.
Default CASESEQ = TRUE.
CASESEC <boolean>
As for CASESEQ, but for secondary structure assignments.
Default CASESEC = TRUE
SMALLSEQ <boolean>
If TRUE, then reliably aligned sequence positions will be large,
unreliably aligned positions will be small.
Default SMALLSEQ = TRUE
SMALLSEC <boolean>
As for SMALLSEQ, but for secondary structure assignments.
Default SMALLSEC = TRUE
POINTSIZE <float>
The pointsize from which the entire alignment will be sized.
Default POINTSIZE = 8.0
VERBOSE <boolean>
If TRUE, then write a lot of comments to the standard output.
Default VERBOSE = FALSE
The output is a new alignment (block) file and an ALSCRIPT command file.