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* [ ] fix extant clades marked as extinct
* [ ] add major subphyla, infraphyla and classes
* [ ] sort cladogram
* [ ] add to classes:
* [ ] ...
i2xzy updated
5 years ago
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**Improvement Description**
Allow collapsing specific taxonomic clades to specific level. E.g., if you want to view some taxa at genus level but collapse others to family level (or even specify the l…
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Dear Author.
I'm using
```
b=[1,2]
st.spatial.trajectory.pseudotimespace_global(adata_SME, use_label="leiden", list_clusters=b)
and
a=[0,2]
st.spatial.trajectory.pseudotimespace_global(adata_S…
zyy23 updated
6 months ago
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For NCBI but also for mutations / clades?
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### Context
Sometimes one wants to use multiple independent clade systems, like clade, outbreak, lineage in monkeypox or whole genome clade and G gene clade in RSV
Right now, augur clades always o…
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Phylotree.js has a "Collapse Subtree" option. We can use this to highlight a particular clade by collapsing all other clades in the phylogeny.
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Taxa of unknown rank or clades will have a wrong scientific name.
For example the Corticata clade is named Eukaryota in the current dwca:
http://en.wikipedia.org/wiki/Corticata
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When I batch load, and I get duplicates, then I want to wipe chunks back out.
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The current method can cause issues on update, including:
- Excess files (minor)
- Incomplete unarchiving (intermediate)
- Incorrect index for clades (major)
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**Background**
When #25 is complete, this hub will have a function that generates a list of clades to be forecast for each modeling round.
The next step is to provided an automated way to schedule a…