STAMP
4.2
dstamp/alscript
Russel, Barton
dstamp
dstamp
perl
dstamp
0
alscript
perl
" ; alscript $prefix.als"
100
alscript_file
$prefix.als
postcript_file
$prefix.ps
aligfile
Alignment file produced by stamp (-f)
perl
" -f $value"
1
This must be a STAMP alignment file, containing both transformations and a sequence alignment. It will not work on transformation files lacking sequence alignment data or STAMP data.
stamp_alig_file
perl
1
prefix
Output file prefix (-prefix)
perl
" -prefix $value"
STAMP
20
stamp_char
The type of STAMP data to be use (-c)
perl
($value && $value ne $vdef)? " -c $value" : ""
G
2
The type of STAMP data to be used (ie. the first letter that occurs after the `#' characters in STAMP multiple alignment output).
threshold
Threshold (-t)
perl
(defined $value && $value != $vdef)? " -t $value" : ""
6.0
2
window
The minimum length of a stretch of reliable regions to be allowed (-w)
perl
(defined $value && $value != $vdef)? " -w $value" : ""
3
2
ignore
Number of sequences that can be ignored during the calculation of residue or residue-property conservation (-ignore)
perl
(defined $value)? " -ignore $value" : ""
2
if ignore = 1 you allow one `error' in one sequence during the calculation of conserved positions
colour
Output will be in colour (-colour)
perl
($value)? " -colour" : ""
2
motif
Write a motif in the space between the sequence alignment and the aligned secondary structures (-motif)
perl
($value)? " -motif" : ""
2