John Huddleston

Thank you, @tsibley! A rebase would be really helpful here. Your comments highlights parts of the align module that are unclear to me, too. We may need to revisit the...

This is still an important feature, but I don't know how important compared to other priorities. I'd either leave this open as the reflection of the issue or convert to...

@tomalf2 Thank you for your patient persistence with this issue! You're correct that augur align has always been implicitly designed for nucleotide sequence input. At the very least, we should...

@jameshadfield This might be better for a future dev chat instead of GitHub comments, but what do you think about using that encoding of uncertainty in the `confidence` field to...

Lower/upper would cover most cases. It could be useful to have a way to represent "samples" from a distribution to be plotted instead of a range of values, in the...

+1 for the feature and for `--alignment-builder-args` (unsurprisingly, since I originally recommended this). I don't have strong feelings about the argument name, really, but I have a slight tendency to...

The cause of this bug seems to be the same as the cause of https://github.com/nextstrain/augur/issues/1711, too: the fact "clades" aren't defined by hierarchical relationships but through inheritance of allele definitions...

I just ran into this issue where I wanted to know how many test viruses were represented by a mean/std line in the measurements panel for one clade (the blue...