Abstract: Provided herein are methods of generating codon optimized nucleotide sequences. The methods include reverse-translating a target amino acid sequence multiple times to generate a plurality of candidate codon optimized nucleotide sequences in which a given codon is randomly selected from synonymous codons encoding a given amino acid residue and incorporated into a given candidate codon optimized nucleotide sequence in the plurality of candidate codon optimized nucleotide sequences. The methods also include determining a total number of occurrences of problematic nucleotide sequences in each of the candidate codon optimized nucleotide sequences to generate a problematic nucleotide sequence count for each of the candidate codon optimized nucleotide sequences. In addition, the methods also include identifying candidate codon optimized nucleotide sequences that comprise a lowest problematic nucleotide sequence count. Additional methods as well as related systems and computer readable media are also provided.