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]:

Mandatory qualifiers:

[-sequence] (seqall)

Sequence database USA.

[-outfile] (outfile)

Output filename.

Advanced qualifiers:

-cfile (codon)

Codon usage table name.