codon usage bias and growth rate

[sarabeier]

Hi Anamaria,
I would like to suggest you to incorporate also the work on codon usage bias and its linkage to growth rate in genomic/metagenomic data as introduced in Vieira-Silva & Rocha (https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1000808) into the coRdon package. This would include the parameters ΔENC'/ΔENC'a S/Sa, F, and d.
Kind regards, Sara

[maurijlozano]

Helo 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]

See #8