Zheng Ruan

I agree. This would be very helpful to speed up the training step. Any estimate when this feature will be implemented?

The `default_codon_table` does not contain the information for translating ambiguous codons. You can manually add such piece of information to the `default_codon_table` by specifying the following code. ``` default_codon_table.forward_table['CCR'] =...

The `codonalign.build` function doesn't support ambiguous dna right now. Internally, it maps each amino acid to its codon using a re expression dictionary based on user specified codon table. Since...

Yes, you can modify the codon table by adding all desired ambiguous codon to amino acid mapping.

I have an idea to incorporate ambiguous codon alphabet into the current code set. This could be a user specified option in future release. I will see if I can...

Hi @universvm, If you update your biopython to the latest version in github, the the unexpected keyword argument `codon_table` error should not occur [(see here)](https://github.com/biopython/biopython/blob/master/Bio/codonalign/codonalignment.py). `get_dn_ds_matrix()` now accepts `codon_table` argument....

The `codonalign.build` used to be able to handle ambiguous nucleotide. But since we dropped the Alphabet class altogether in biopython recently, this is not functional again. One solution might be...

I hereby give my explicit permission to switch to the BSD 3-clause license.

I agree that it is a good idea to officially release the module. The basic function of `Bio.codonalign` is sufficiently stable and many bugs have been fixed over the past...

Hi @mdehoon, The main function that `Bio.codonalign` provides is to generate alignment of codons based on a protein sequence alignment and the corresponding DNA sequences that encode the protein sequences....