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Currently clades are defined independently of one another in the provided TSV, but we often duplicate the mutations of a parent clade. For example, 21L is a descendant of 21M so we have the following:…
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BA.2 + Spike T833I
S:T833I substitution has been observed in Alpha and other lineages too (from Cov-Spectrum) - 1410 sequences in total:
B.1.1.7 (33.19%) BA.2 (13.83%) BA.1.1 (7.45%) BA.1 (7.16%)
…
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Hello！
I wonder if “p__Bacteria phylum [Proteobacteria/Bacteroidetes]” in the classification report represents a new phylum that has not been discovered before. Similarly，for “f__Caulobacterales fam.…
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Your graph in https://nextstrain.org/ncov/gisaid/global is inspiring. Could you kindly suggest how you infer their parent/child relationships? Related code or paper will be a great help!
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It'd be nice if one could download fastas corresponding to an open=Genbank query directly from covspectrum.
This would be a nice addition to the "sequence list" that provides EPI_ISLs etc but no fa…
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Hello, I'm attempting to run the 'make preprocess' command but receiving the error shown below.
/pyro-cov$ make preprocess
python scripts/preprocess_usher.py
34644 Refining a tree with 3009…
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BPO | [9221](https://bugs.python.org/issue9221)
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Nosy | @merwok, @tiagoantao
*Note: these values reflect the state of the issue at the time it was migrated and might not reflect the current…
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I'd like to download multiple sequences in one go using the fasta endpoint.
However, I can't find any details in the specification about how to select multiple accession numbers. If I simply add mu…
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Hi,
I recently found a duplicate taxon ID for genus Leptothrix, which is a genus name for bacterial species as well as for Leptothrix hardyi, a spider species. Spiders are interesting species, but …
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### Please complete the following tasks
- [X] I have searched the [discussions](https://github.com/clap-rs/clap/discussions)
- [X] I have searched the [open](https://github.com/clap-rs/clap/issues…