james hadfield

I think this proposal should work & will be a very useful addition 👍. My recommendations for the implementation: * Define a node-name-regex (e.g. `NODE_` + _n_ character hash or...

Hi @razsultana -- as far as I'm aware no progress has been made on an implementation. For an immediate solution you could manually label the nodes you wish to zoom...

Let's at least add the deprecation warning. It's good practice to leave things around for a while after the warning appears, so that'll give us plenty of time to decide...

I'm having trouble reproducing this. I've created a small tree to try to reproduce, which flags up some oddities, but I can't reproduce a duplicated gap region. Could you identify...

Hey @AngieHinrichs - @joverlee521's summarisd things perfectly but note that the segmented annotations can't yet be produced by the augur tools so you'll have to add them via a short...

> This PR makes augur translate output the correct annotation for complex CDSs I think you mean `augur ancestral`? Changes here are to `ancestral.py` and as far as I can...

Great suggestions -- thanks @Xkeeper0. Would you mind breaking these out into separate issues? Hopefully we can get people to help submit PRs for each of them. One quick point...

Revisiting this with fresh eyes I'm going to close this PR -- the introduced functionality is either available in existing augur commands (`augur align --fill-gaps`) or is pathogen-specific and can...

Revisiting this I think documenting the functionality we have is the better way to solve this, and have done so via [this PR](https://github.com/nextstrain/docs.nextstrain.org/pull/158).

This should be solved shortly with the merge of #728. This will allow you to specify the key for nodes which belong to the clade via `--membership-name` as well as...