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**Description**
**Sub-lineage of:** KP.2.3
**Earliest sequence:** 2024-6-20 – India (travel to USA, Washington state Airport), EPI_ISL_19229712
**Most recent sequence:** 2024-7-7 – India (travel to…
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### Context
The glycoprotein complex (GPC) is the only surface protein of the Lassa virus (LASV) and plays a crucial role in mediating entry into host cells. It is also a primary target for neutr…
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Found with @aviczhl2 's phylogenic tree analysis tool.
JN.1.29.1> C8917T> G22599C(S:R346T)> G18318T, C20930T(Orf1b:T2488M)> A259G, A28984G> T21728G(S:L56V)
Query: C8917T, A9935G, G22599C, -A405G
…
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Hello!
I'm testing vRhyme and got stuck after 'Performing machine learning classification' step
Running on a slurm HPC system
Fresh mamba install
Inputs :
a) Single-end Next-seq reads;
b) vir…
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For tree sequences inferred from simulations, we can't directly compare inferred dates to true dates because node sets differ between the inference and the simulation.
Instead, we've been looking …
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Variants of this issue may have been mentioned in other issues, so sorry if it is a duplicate. The standard database build looks like it is trying to `overwrite 'assembly_summary.txt'` which triggers …
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Just two sequences but featuring four spike mutations worth proposing it here.
Defining mutations:
XDV.1.8 >> T9892G > A23971G > G6183A (rev, real?) , T9142C (rev, real?), A9715T, Orf1a:A3615V (C…
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Currently the formatting of the help messages (defined via the leading docstrings at the start of each script in `augur/*.py`) is not respected by `augur --help`. We should improve this which will en…
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Partitions are listed among other tables, leading to a very noisy list.
The relations can be easily listed, in Postgres, by
```
SELECT *
FROM pg_partition_tree('action_gateway');
```
BTW, M…
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Dear Dr Loytynoja,
This is Francesco from the university of Innsbruck. I'm trying to use prank to align coding mtDNA sequences, but prank is giving me bad jokes. The program works perfectly with th…