CUO (Codon Usage Optimizer) is a GUI-based multiplatform software written in Java. The main function of the software is to optimize genes to be transformed into the Chlamydomonas reinhardtii chloroplast genome using an original set of algorithms for calculation, data processing and automated reasoning.Furthermore, it can be used as an electronic drawboard for gene sequence analysis and design. While the software focuses on the C.reinhardtiigenome, it can also be used to optimize genes into other hosts as well.Since E.coli and S.cerevisiaeare frequently used in the industry of biotechnology they will be the focus of the software in near future.