The Codon Adaptation Index (CAI) is a measure of the synonymous codon usage bias for a DNA or RNA sequence. It quantifies the similarity between the synonymous codon usage of a gene and the synonymous codon frequency of a reference set. Extreme values in the nucleotide or in the amino acid composition have a large impact on differential preference for synonymous codons. It is thence essential to define the limits for the expected value of CAI on the basis of sequence composition in order to properly interpret the CAI and provide statistical support to CAI analyses. Though several freely available programs calculate the CAI for a given DNA sequence, none of them corrects for compositional biases or provides confidence intervals for CAI values.
Puigbò, P., Bravo, I. G., & Garcia-Vallvé, S. (2008). E-CAI: A novel server to estimate an expected value of Codon Adaptation Index (eCAI). BMC Bioinformatics, 9. https://doi.org/10.1186/1471-2105-9-65