scopalign generate alignments for families in a scop classification file by using STAMP.
Here is a sample session with scopalign:
% scopalign
Name of scop classification file (EMBL format input).
Location of scop structure-based sequence alignment files (output).
Extension of scop structure-based sequence alignment files (output).
Location of scop structure alignment files (output).
Extension of scop structure alignment files (output).