How does coRdon calculates CAI?

[maurijlozano]

Dear Anamaria
I wanted to ask you how the CAI is calculated by coRdon because I'm getting different values with other programs using the same reference set. Additionally I'm getting values greater than 1 and that should not be possible.
Thank's
Mauricio

[anamariaelek]

The minor differences might come from using different "pseudocount" values for codons not used in the reference set (in coRdon this is 0.5, however in some implementations this is 0.01). The chosen values reflect the fact that coRdon was written to output the results compatible with INCA, a legacy tool previously developed in the group. I imagine this might also cause some of the values to exceed 1, contrary to the original CAI definition.

For the implementation, see here.

[maurijlozano]

OK, thank you for your answer.