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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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From https://github.com/sars-cov-2-variants/lineage-proposals/issues/1509
Other than KP.1.1.1(S:K182N), other seqs on the Orf1b:L2213F branch of KP.1.1 have another NTD mutation set that usher does…
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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…
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### What client do you play on?
enUS
### Faction
Both
### Content Phase:
70
### Current Behaviour
They are not casting Ice Tomb to the target highest on threat, but randomly
http…
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From branch 110 of https://github.com/sars-cov-2-variants/lineage-proposals/issues/1253
JN.1+C19374T+S:F456L
Query: C19374T, T22928C, T3565C,-17334,-7113
No. of seqs: 21
First: EPI_ISL_18924257, …
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KP.1.1.1+C10341T, G21800T, C26078T(Orf1a:P3359L,S:D80Y,Orf3a:T229I)
GISAID query: G21800T, A22108C, G17334T
No. of seqs: 24(USA 23 UK 1)
First: EPI_ISL_19145490,USA, 2024-3-19
Latest: EPI_ISL_…
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KP.1.1.3+C3992T+C25350T(S:P1263L)
GISAID query: C3992T, C4999T, C25350T,del21653
No. of seqs: 7(USA 5(2 from UK), Spain 1 UK 1 )
First: EPI_ISL_19153965, USA, 2024-5-3
Latest: EPI_ISL_19254598…
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I was just trying to use Usher and got the following server error (both for usher.bio and dev.usher.bio [the test server]):
>Couldn't connect to database hgcentral on hgnfs1-c as hgcentuser. Can't …
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In the newest usher tree the placement is altered and JN.1.39.1 now starts from a weird A16011G node.
[usher](https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice10_genome_t…
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After LB.1.3.2/MH.1 have been designated there is another LB.1 FULL QUAD to track
LB.1 with S:S31del> S:T572I (C23277T)
Query:Del21653,C23277T,G22111T, -C7869T,-C18131T,-C5770T,-C13721T,-C4784T
…