cusp reads one or more coding sequences (CDS sequence only) and calculates a codon frequency table. The output file can be used as a codon usage table in other applications.
Here is a sample session with cusp, using just one sequence. For normal use, extract a set of coding sequences and use them as input:
% cusp -sbeg 135 -send 1292 Create a codon usage table Input sequence: embl:paamir Output file [paamir.cusp]: