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This todo can now be done AFAICT
https://github.com/nextstrain/conda-base/blob/224ad3997cc7ca17fa6fa2ed29ade37c21b3fece/.github/workflows/ci.yaml#L149-L152
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:cool:
### :pushpin: Explain the Request
Add mutation context to the Mpox track of the Augur_PHB workflow.
### :books: Context
In Nextstrain, users have the option to annotate the Mpox tre…
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Ideas here came out of discussion with @tsibley in our 1:1 regarding https://github.com/nextstrain/.github/pull/62#issuecomment-2105402378. This would supersede #63 + #62.
## Proposal
With the …
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Lineage B.1.20 is diverse and seems to be expanding in several countries. This proposal is for a new sublineage B.1.20+OPG188:E12K observed in USA and Germany total of 31 sequences from NCBI (soon to …
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Second proposal for a sublineage of B.1.20. The proposed sublineage is found in USA from public data but soon there will be more from Australia.
![Screenshot from 2024-06-03 14-20-17](https://githu…
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### Context
Following the naming pattern set in SARS-CoV-2 sequences, strain names are usually `//`. All three fields are typically available in the metadata so we can concatenate them to "build" a r…
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Please place an "x" in all the boxes that apply
---------------------------------------------
- [X] I have the most recent version of this package and R
- [X] I have found a bug
- [X] I have …
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Maybe add mpox to start page, similar to how Nextstrain displays the kind of trees one can see on the start page - would help discoverability etc.
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Only SARS-CoV-2 has pango lineages per se, there's something a bit like pango for mpox, and similar (but different) systems for flu, rsv etc
Is the lineage config field required? That would not mak…
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In the last of a 7-contig monkeypox genome assembly, RATT produces a feature like this one at the top:
```
FT repeat_region complement()
FT /note="ITR"
FT …