Codon usage bias (CUB) is pervasive in genomes. Studying its patterns and causes is fundamental for understanding genome evolution. Rapidly emerging large-scale RNA and DNA sequences make studying CUB in many species feasible. Existing software however is limited in incorporating the new data resources. Therefore, I release the software CUA which can compute all popular CUB metrics, including CAI, tAI, Fop, ENC. More importantly, CUA allows users to incorporate user-specific data, such as tRNA abundance and highly expressed genes from considered tissues; this flexibility enables computing CUB metrics for any species with improved accuracy. In sum, CUA eases codon usage studies and establishes a platform for incorporating new metrics in future. CUA is available at http://search.cpan.org/dist/Bio-CUA/ with help documentation and tutorial.