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Hi,
I am trying to convert a West Nile virus auspice tree to a MAT. The `matUtils extract` keeps including "NC_045512" in the output file, but it's not in my input auspice file.
`matUtils extrac…
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From https://github.com/sars-cov-2-variants/lineage-proposals/issues/1253
Branch 11: 368 seqs (4 in 2023 and 364 in 2024)
[usher](https://cov-spectrum.org/explore/World/AllSamples/Y2024/variants?nuc…
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Hi, I wrote an open-sourced usher analyse tool that can automatically highlight important lineages in usher-processed jsons. Hope it can help everyone find and analyse new lineages more quickly, espec…
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In order to simplify `Room`s, I'd like us to get rid of the `locked` / `internal` etc. distinctions and instead leverage a piece of Furniture.
## Fauxsonas
- Guest - Unauthenticated `Person`
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Loading a large tree (SC2 Usher) takes quite a while (~1min) even on fairly performant hardware (M1 Pro 32GB).
I can imagine that gzip decompression might be a bottleneck - zstd decompresses much f…
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KP.2+C15579T+C21998T(S:H146Y)
GISAID reads this mutation as T21994C+del21998_22000, resulting in S:H146del instead of the S:Y144del for normal JN.1*s.
However, starting from S:Y144del, usher's S:…
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From branch 99 of https://github.com/sars-cov-2-variants/lineage-proposals/issues/1253
JN.1+T17859C+C3172T+S:R346T,F456L
Query: T17859C,T22928C,T3172G,T3565C
No. of seqs: 22 on UShER (Portugal 4 S…
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I just tried to follow the installation instructions at https://usher-wiki.readthedocs.io/en/latest/QuickStart.html I tried three things, none of which worked.
1. Following the Quick install comma…
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### Context
IQtree can struggle with large trees and take long. We may want to experiment with using Usher and/or Maple as alternatives. They probably are significantly faster and may be good enough …
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KP.4.2+A15171G+T21740C, A29700G(S:S60P)+A17637G,T22197C(Orf1b:P2313S,S:I212T)
This branch suddenly emerges in multiple countries, deserve watching.
Note that the S:I212T is read as S:N211T+S:L21…