Zheng Ruan

@mdehoon Yes. this is usually the case. This type of analysis used to be very popular to study the gene evolution within a population.

@mdehoon I'm happy to review the tutorial section of using `Bio.Align` module to handle codon alignment. The most important function is `Bio.codonalign.build()`, where the input of a protein alignment and...

@mdehoon Are you able to handle multiple sequence alignment as opposed to pairwise sequence alignment? The protein sequence alignment is typically generated by external software, rather than within biopython. Test...

This is great! The `Bio.codonalign.build()` is more rigorous as it can also handle mismatches and non-coding sequences. For example: ``` from Bio.SeqRecord import SeqRecord from Bio.Seq import Seq from Bio.Align...

@mdehoon What you described is generally true. However, there are situations where users may want to focus on the protein alignment instead of nucleotide sequences. For example, if only a...

> _If_ that is the case (GPL violation), it would be an even stronger reason to drop the experimental `Bio.codonalign` in favour of the more recent work in `Bio.Align`. >...