chips calculates Frank Wright's Nc statistic for the effective number of codons used.

Here is a sample session with chips. If the sequence extends beyond the coding region, the start and/or end positions of the CDS must be provided. chips analyzes only protein coding regions:

% chips -sbeg 135 -send 1292
Input sequence: embl:paamir
Output file [paamir.chips]:

Mandatory qualifiers:

[-seqall] (seqall)

Sequence database USA.

[-outfile] (outfile)

Output filename.

Advanced qualifiers:

-cfile (codon)

Codon usage file.