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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/1856
In the new usher update it moves most of the previous KP.3.1.3 seqs to KP.3.1+G25644T+S:S31F branch. This shall be the cor…
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KP.3.1.1+G5230T(Orf1a:K1655N)+C853T+A22106G(S:K182E)
GISAID query: G5230T,C853T,A22106G
No. of seqs: 25(USA 1 Japan 2 New Zealand 1 Australia 21(SA, QLD, NSW))
First: EPI_ISL_19305166,2024-7-12…
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KP.2.3+del21653_21655(S:S31del)+C28714T+C18555T+C9298T+C22329T(S:S256L)
GISAID query: C22329T, C9298T, C18555T
No. of seqs: 23(USA 22(1 from Burkina Faso) China 1(from USA))
First: EPI_ISL_1929…
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LB.1.3.1+A28412T(N:N47Y)+T17919C+C22329T(S:S256L)
GISAID query: C22329T,T17919C,A28412T
No. of seqs: 6(Germany 1 USA 1 Canada 1 Netherlands 1 Israel 2)
First: EPI_ISL_19316639, Germany, 2024-7-…
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LF.8.1.1+C13436T+A27300G+A22995C(rev)
GISAID query: C13436T,A27300G,-22995
No. of seqs: 3(USA , 2 from Qatar)
EPI_ISL_19362364, 2024-8-19, USA-VA
EPI_ISL_19375171,19375176, 2024-8-23, USA f…
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Take from CogSci paper with Jan. Since it worked pretty well, this would be a nice network to showcase some larger dynamical examples potentially.
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From branch 7 of https://github.com/sars-cov-2-variants/lineage-proposals/issues/1771
LB.1.7+C22096T+S:R190S
Query: G22132T, C4784T,del21653,C22096T
No. of seqs: 11 (USA)
First: EPI_ISL_19177717, …
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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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Write down some details about deduplicating sample sequences and MAFFT alignment (version and options).
szhan updated
2 weeks ago