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Currently neuraminidase clades are being classified at a depth that does not show the full scope of genetic diversity. Neuraminidases need to be reclassified by splitting up current clades. After recl…
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* [ ] Ward linkage (currently broken)
* [ ] Optimize single linkage with slink (https://sites.cs.ucsb.edu/~veronika/MAE/summary_SLINK_Sibson72.pdf)
* [ ] Support median and centroid linkage (https:/…
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Dear @emmahodcroft
It is unclear to me where the information information in the following files is from:
* genome/config/clades.tsv
* vp1/config/clades.tsv
I suspect these are downloaded and …
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When you just pass the input-fasta URL param, Nextclade web autostarts the analysis, but it shouldn't.
It should instead just load the sequences and do auto-dataset-detection
Repro:
1. Load ht…
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It would be good to explicitly validate the clades.tsv file and give a helpful error message if it doesn't conform to expectations.
This would help users like this one, who opened issue https://git…
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It would be great if there was a selection possible which monkeypox dataset to use for the Nextclade integration.
Right now, mpxv is the only option, but for most sequences this is not the best cho…
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### Setup
I am reporting a problem with Biopython version, Python version, and operating
system as follows:
```python
[GCC 4.4.7 20120313 (Red Hat 4.4.7-1)]
CPython
Linux-4.4.0-43-Microsoft-…
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Hi,
Great work!
Do you think that, if trained, Tiberius will provide equally good results for other groups of organisms other than mammals? Such as in large invertebrate genomes?
Also, do yo…
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### Author(s) of proposal
Li-Bing Zhang, Xin-Mao Zhou
### Name of taxon
Calligrammitis, Devolia, Glabrigrammitis
### Rank of taxon
Genus
### Approximate number of species affected
5
### Descri…
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[Bloom et al. (2023) MBE](https://academic.oup.com/mbe/advance-article/doi/10.1093/molbev/msad085/7113660) examined clade-specific mutational spectra. In Figure 1, they compared VoC-specific mutationa…