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.

Sequence Analysis in a Nutshell
Sequence Analysis in a Nutshell: A Guide to Common Tools and Databases
ISBN: 059600494X
EAN: 2147483647
Year: 2005
Pages: 312

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