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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
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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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Noting error in the automated genbank/clade-counts workflow:
- [2024-07-23](https://github.com/nextstrain/forecasts-ncov/actions/runs/10069513692)
- [2024-07-24](https://github.com/nextstrain/foreca…
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**Background**
On the date of model input data processing, we want to save some metadata about the current nextclade SARS-COV-2 dataset (i.e., the most current dataset listed when running `nextclade …
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Hey guys,
Thank you for the great tool. I was using the tool to look over some kraken2 results and was unsure what the Clade counts vs Taxon counts meant. I see the read numbers for both these option…
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## Description
[Originally discussed in Slack](https://bedfordlab.slack.com/archives/C2G8C5LUD/p1643305652009300?thread_ts=1643246971.008600&cid=C2G8C5LUD) and [in GitHub comments](https://github.c…
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# Feature Request: Comprehensive Export/Import Functionality for Datalake Table Management
## Overview
First and foremost, thank you for your incredible work on the seafowl project. Your efforts i…
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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 schedu…
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Clades, whether using a maximum or minimum clade definition, may be defined as [crown-clades](https://en.wikipedia.org/wiki/Crown_group) or [total clades](https://en.wikipedia.org/wiki/Crown_group#Pan…
hlapp updated
3 years ago
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Attempting to use dnConstrainedTopology() with a dnUniformTimeTree() tree distribution results in a segfault.
**To Reproduce**
```
taxon_names = ["tax1", "tax2", "tax3", "tax4"]
for (i in 1:…