CUBAT is a python program to help analyze codon usage bias(CUB). You can run it as a script or the command line.
For install:
pip install cubat
For update:
pip install cubat --upgrade
You can easily calculate multiple codon bias indexes with CUBAT.
For example: You want calculate CAI(with reference of human), ENC and RSCU of SARS-COV-2. All you need to do is provide a fasta file of SARS-COV-2 and human reference for cai(You can use the built-in data).
Run this:
cubat analyze --cr example/cai_ref.csv -erc Test_Data/Sars_cov_2.fasta
You will get two csv sheets with your desired results there.
The following is a comparison with other software that can calculate CUB indexes.
| 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) | √ | √ | ||
| CBI(codon bias index) | √ | √ | √ | |
| Fop(frequency of optimal codons) | √ | √ | √ | |
| TAI(tRNA adaptation index) | √ | |||
| CSC(codon stabilization coefficient) | √ | |||
| the scaled χ2 | √ | |||
| Amino acid usage | √ | √ | √ | |
| Codon table replaceability | √ | √ | ||
| cross-platform | √ | √ | √ |