alphabet ={DNA|RNA|Protein|Binary|Word(letter={DNA|RNA|Protein},length={int})| Codon(letter={DNA|RNA}, type={Standard|EchinodermMitochondrial|InvertebrateMitochondrial|\ VertebrateMitochondrial})} The alphabet to use when reading sequences. DNA and RNA alphabet can in addition take an argument:
bangAsgap={bool}Tell is exclamation mark should be considered as a gap character. The default is to consider it as an unknown character such as ’N’ or ’?’.
genetic_code = {translation table}Where ’translation table’ specifies the code to use, either as a text description, or as the NCBI number. The following table give the currently implemented codes with their corresponding names:
| Standard | 1 |
| VertebrateMitochondrial | 2 |
| YeastMitochondrial | 3 |
| MoldMitochondrial | 4 |
| InvertebrateMitochondrial | 5 |
| EchinodermMitochondrial | 9 |
| AscidianMitochondrial | 13 |