John Huddleston

Thanks, @bqminh! Based on the IQ-TREE docs, it looks like Augur might support CMAPLE already by passing custom arguments to IQ-TREE like `augur tree --tree-builder-args="--pathogen-force"` (where IQ-TREE is already the...

@corneliusroemer Can you say a little more about why the current `augur traits` command isn't a good solution to the problem? From this PR, it looks like some of the...

Thanks, @corneliusroemer. I see now how different this logic needs to be from `augur traits`. We recently discussed [using Nextclade to assign clades in the seasonal flu workflows](https://github.com/nextstrain/seasonal-flu/issues/131), too, which...

I chatted with @tkanderson today at Options and he upvoted this feature request as high priority for their work. He is interested in the full nextflu functionality where the tree...

Thanks for documenting this so clearly, @victorlin. I'm definitely in favor of preferring `--output-sequences` for users and eventually deprecating `--output`.

This issue also affects recent 6-month H1N1pdm HA trees where [subclade D.2 gets nested within subclade D.3 because of a recurrent clade-defining substitution](https://nextstrain.org/seasonal-flu/h1n1pdm/ha/6m@2025-04-02?branchLabel=Subclade&c=subclade&label=Subclade:D.3). This specific case would make a good...

Thanks, @victorlin! I like `--keep-ids` and your proposed implementation. It will probably take longer to write the tests than the desired functionality... 😄

> decide what values you want to allow in auspice, potentially dictated by any URL query constraints I'd vote for at least hyphen, underscore, and spaces to be added to...

That sounds reasonable!

@genehack Thanks for checking! This issue is still relevant and desirable, although only for a small group of users (maybe only me), so it is still relatively low priority. If...