My paper describing the software CUA is deposited into BioRxiv at http://dx.doi.org/10.1101/022814 now. The software is at http://search.cpan.org/dist/Bio-CUA/.
If you want to compute codon usage bias metrics (tAI, CAI, ENC, Fop) in any species, this is the only software you need. Please try the tutorial and learn how to use it.
Welcome comments and suggestions.