What are the steps to calculate Codon Adaption Index using codonw? How to give reference set of genes to the codonw software? Other than codonw, is there any other software that computes and gives CAI? Also, is there any software that calculates CAI using Carbone's method?
If you happen to be interested in yeast, I downloaded the CAI values from a supplemental table from this paper:
with my analysis discussed in this paper:
If you aren't interested in yeast, perhaps the Drummond et al. paper can at least provide some helpful pointers.
While Running codonW, it automatically generates the reference set ie potential gene. u can use these data for your cal analysis.
It generates files like cai.coa, fop.coa, cbi.coa you can use these file for corresponding analysis.
for your questions, you can use cai.coa file as the reference set for CAI calculations.
For those interested in calculating codon usage statistic, including CAI, there's our R/Bioconductor package that lets you do this, and it comes with some nice visualisations, too https://bioconductor.org/packages/release/bioc/html/coRdon.html