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This work began as https://github.com/nextstrain/nextstrain.org/pull/170, but post-migration will need another look here. The idea was merging / reducing any duplication between:
1. https://nextstrai…
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Hello,
For our research, I have been using resources from Nextstrain and I encountered an ambiguity that I wanted to ask about.
I am currently working on the tabular file for nuc conversions bel…
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**Stephen Owen** 6 months ago
Discussion in data entry advanced today (26/5/18). The current option for a species or subspecies, is both free text and duplicate allowable. Needs to necessitate at lea…
i2xzy updated
5 years ago
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### Context
When the clades.tsv is messed up, augur 22.0.1 throws an unclear error: `KeyError: 'gene'`
### Description
Let's catch it and report that something seems up with the clades.tsv
Cur…
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Make comparable syntax and identical taxonset IDs available for the following inference items:
- [ ] `geography` → `sampling_points`
- [x] `model` → `reconstruct_at`
- [ ] Monophyly constraints
…
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function: given a set of species with its corresponding sequences and a phylogenetic tree, return the monophyletic species in the phylogenetic tree
example:
input:
species --> each (a,b,c) is follo…
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Hi!
**Context**: running `make.prosse` on this phylogeny [phylo_incipient.tree.zip](https://github.com/user-attachments/files/15903207/phylo_incipient.tree.zip)
**Error**:
```
Error in edge[ma…
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// tre is the phylocanvas JS object
tre.getSelectedNodeIds()
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Empress is great at coloring the tree when there are comparatively few metadata categories, but if there are lots (e.g. coloring a tree by genus-level taxonomy) then it becomes really hard to glean an…
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### Feature Request
This issue is a solicitation for feedback on an idea.
I've been working on the [RSV pipeline](https://github.com/CDPHE-bioinformatics/CDPHE-RSV) and reusing tasks from this r…