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**Background**
When generating and saving a list of clades to model, we should also get and save information that would be required to get the reference tree in use at the time (for reproducibility).…
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Update the in-progress `make_round_config.R` script to create a new version of `tasks.config` that contains the a new round based on the latest list of clades in `auxiliary-data/modeled-clades`
Defin…
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**Current Behavior**
Given the error, I inspected the [pango-consensus-sequence-summary.json](https://raw.githubusercontent.com/corneliusroemer/pango-sequences/main/data/pango-consensus-sequences_…
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### Current Behavior
Augur export converts literals to lower case in its stderr output - which is probably not what we want
### Expected behavior
Literals are output as they are, not changing cas…
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Hello, I working on combining this method with kernel machine tests. We only want to test on clades with 20 or more leaf nodes. I feel that this should be a simple if else statement, but I am having a…
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In previous versions of OneZoom we had the concept of a "fake" leaf that represented a number of species, e.g. see the comment at
https://github.com/OneZoom/OZtree/blob/e32b3a76a6959460cf31d809143a…
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Hi,
Do you provide any resource for the list of mutational changes per clade?
In the dataset that is acquired with Nextclade CLI, `nextstrain/sars-cov-2/wuhan-hu-1`, there is this statement in R…
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Right now, the `y_i` renaming of internal nodes is a bit jarring.
Perhaps we should enable renaming of only internal nodes that don't have names with something like `clade_i`.
The one thing to wat…
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Collapse subtree into clades that reflect taxa composition
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Has Mpox clade I been designated as Clade Ia and Clade Ib? And is this being reflected in the nextstrain? If so, what mutations are considered? Please, assist. Thank.
Walter