cai calculates the Codon Adaptation Index. It is a simple, effective measure of synonymous codon usage bias.

Here is a sample session with cai:

% cai embl:AB009602
CAI codon adaptation index
Codon usage file [Eyeastcai.cut]:
Output file [ab009602.cai]:

Mandatory qualifiers:

[-seqall] (seqall)

Sequence database USA.

-cfile (codon)

Codon usage file.

[-outfile] (outfile)

Output filename.