There are several ways to view STAMP alignments in a more readable
form than the BLOCK output format. The output files can be read by
the Jalview alignment editor (available from http://www.jalview.org).
Alternatively, BLOCK format files can be converted to other alignment
formats using the ACONVERT tool as discussed previously.
In addition, the STAMP package contains additional programs for
converting STAMP output into a horizontal alignment format and
creating input files suitable for creating figures of
multiple sequence and structure alignments:
VER2HOR reads STAMP output files and displays the alignments in a horizontal text
format.
DSTAMP converts BLOCK format files
into input for GJB's program ALSCRIPT, which can then be used to generate figures
of alignments in Postscript format. Details of DSTAMP and how to obtain
ALSCRIPT are given in CHAPTER VI. DSTAMP determines reliable regions given a set of criteria, and
highlights sequence and secondary structure accordingly.
GSTAMP reads STAMP outputs and creates input suitalbe for creating
molecular graphics figures using Per Kraulis' program MOLSCRIPT.
One simply runs TRANSFORM on a STAMP alignment file, and then run GSTAMP on the same file
to create a MOLSCRIPT input file which will produce separate Postscript files
for each aligned structure, with structurally equivalent regions
shown as ribbons, the rest as
trace.