Codon adaptation index (CAI) is one of them. To examine the CAI value of a gene, a reference table of RSCU (relative synonymous codon usage) values for highly expressed genes is compiled.
A software call CodonW, you can download it from: http://codonw.sourceforge.net/. There is also a PhD thesis associated to it.
shenzy@shenzy-ubuntu:~/Downloads/CondonW/codonW$ codonw input.dat -all_indices -c_type 2 -f_type 4 -nomenu
eg:
shenzy@shenzy-ubuntu:/winxp_disk2/shenzy/circos/work$ codonw Dehalococcoidessp.BAV1.cds.fasta.dat -all_indices -c_type 2 -f_type 4 -nomenu
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