John Huddleston

As a separate note for the rest of the Nextstrain team, @joverlee521 pointed out that we should be able to fix this issue of clades files getting stale by defining...

Ah, I'm sorry, @RasmusKoRiis, I should have provided another test than checking the end of the file; the J.4 clade is older than J.2.4 which appears in the earlier in...

Thank you for these screenshot examples, @RasmusKoRiis. Based on that second figure, I suspect the issue is still that there aren't enough J.2.4 samples to get ancestral sequences that augur...

The main advantage to switching to the new `refine` functionality would be to simplify the workflow a bit and remove an unnecessary accessory script. It's definitely not a high priority,...

Closing in favor of https://github.com/nextstrain/seasonal-flu/issues/234. See https://github.com/nextstrain/seasonal-flu/issues/178#issuecomment-3010444384 for more context.

It's probably not useful now. Generally, I just need a way to quickly annotate proposed subclade annotations through Nextclade for the two frequency estimation methods we're using now. In the...

Another example issue with `augur clades` annotations that appeared recently in our 6-month trees is when older clades have died out and their clade-defining mutations reappear in new clades, those...

Testing this again today with 6-month trees for H1N1pdm HA and NA, I found no issues with the HA assignments (all were consistently monophyletic), but the NA assignments had many...

Thank you, @victorlin and @joverlee521! I actually created the file in this PR by parsing that clade display names YAML! 😄 It turns out the original poster in the nowcasting...

After our recent conversations internally and with @dpark01 about reducing the complexity of the ncov workflow and improving the portability of the existing workflow with other workflow languages and/or platforms,...