ancestral: update module docstring to include amino acids

[joverlee521]

Description of proposed changes

Update ancestral's module docstring to include new feature of inferring amino acid sequences.
Added based on my understanding from reviewing #1258.

Please feel free to elaborate or correct any inaccuracies.

Checklist

• [ ] Add a message in CHANGES.md summarizing the changes in this PR that are end user focused. Keep headers and formatting consistent with the rest of the file.

[joverlee521]

A potential question that came to mind when I was writing this:

Should we warn users that nucleotide sequences and amino acid sequences are inferred separately? From my understanding, they are never cross checked within augur ancestral so there could potentially be mismatches between the nucleotide and amino acid mutations.

[jameshadfield]

Should we warn users that nucleotide sequences and amino acid sequences are inferred separately?

Yes - good idea. One nice aspect of having them both in the same command like this is that we can adopt a codon-aware reconstruction in the future. If we end up parsing annotation files within augur ancestral (as part of #1280) then we could easily test out how often the two reconstructions are contradictory.

[huddlej]

Thank you for catching this omission from the original PR, @joverlee521! This looks good to me as it is, but would you think to add the warning you mention in the comments to this section?