CoDe is a tool to deoptimize the RNA or DNA sequences based on codon usage. Codon-pair deoptimization involves increasing the frequency of underrepresented codon pairs without changing codon usage or amino acid sequences. It is a highly efficient virus attenuation strategy that utilizes suboptimal codon pairs to achieve attenuation of recoded viruses. This tool deoptimizes the RNA or DNA sequence by replacing lowest frequency codon encoding the same amino acid, obtained from organism specific codon usage tables.