Table 1 Summary of codon harmonization/optimization tools and their characteristics
From: An exploratory in silico comparison of open-source codon harmonization tools
NAME | OPEN-SOURCE | INPUTS REQUIRED | FORMAT | CODON… | OTHER REMARKS | REFERENCE |
|---|---|---|---|---|---|---|
GALAXY | Yes | - Genome natural & target host - Nucleotide sequence | Webpage | … harmonization |  | [35] |
EUGENE | Yes | - Genome natural & target host - Nucleotide sequence | Software | … optimization & harmonization | - Several gene redesign options - Time consuming | [34] |
CODON- WIZARD | Yes | - Genome natural & target host - Codon usage table (CUT) - Nucleotide sequence | Software | … optimization & harmonization | - Several gene redesign options | [36] |
CHARMING | Yes | - CUT natural & target host - Nucleotide sequence - Codon usage measure - Window size | Webpage/Software | … harmonization | - Downloadable Python code - Equally well harmonized synonymous outputs possible | [37] |
CAD4BIO BGene | No | - Company contact information | Webpage | … optimization & harmonization |  | [31] |
GeneWiz by Azenta | No | - Company contact information | Webpage | … optimization |  | [46] |
Atum.bio DNA2.0 Gene Designer | No | - Company contact information | Webpage | … optimization |  | [22] |
GeneArt GeneOptimizer Thermofisher | Yes | - Target host - Nucleotide sequence | Webpage | … optimization |  | [47] |