Codon Usage Bias Analysis Toolkit (CUBAT) is a powerful python package for codon usage bias (CUB) analysis. CUBAT can be imported as a module for custom analyses and has a command line interface as well.
You can install cubat with pip from command line:
pip install cubatTo update, run the following command:
pip install cubat --upgradeCUBAT can calculate various indices related to codon usage. Here is a summary of indices supported by CUBAT in comparison with other popular software.
| Indices | CUBAT | codonW | DAMBE | EMBOSS |
|---|---|---|---|---|
| RSCU (relative synonymous codon usage) | √ | √ | √ | |
| Nc (effective number of codons) | √ | √ | ||
| Nc (effective number of codons,SYX13) | √ | √ | ||
| CAI (codon adaptation index) | √ | √ | √ | √ |
| CAI2 (Xuhua Xia,2007) | √ | √ | ||
| TAI (tRNA adaptation index) | √ | |||
| Other Features | ||||
| Codon table replaceability | √ | √ | ||
| Cross-platform | √ | √ | √ |