scopalign generate alignments for families in a scop classification file by using STAMP.

Here is a sample session with scopalign:

% scopalign

Mandatory qualifiers:

[-scopf] (infile)

Name of scop classification file (EMBL format input).

[-path] (string)

Location of scop structure-based sequence alignment files (output).

[-extn] (string)

Extension of scop structure-based sequence alignment files (output).

[-pathc] (string)

Location of scop structure alignment files (output).

[-extnc] (string)

Extension of scop structure alignment files (output).