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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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It seems that issues with the server used for training the model of pangoLEARN (https://github.com/cov-lineages/pangolin-data/releases/tag/v1.19) cannot be solved in a short time. Besides, an assignme…
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From https://github.com/sars-cov-2-variants/lineage-proposals/issues/1666
GISAID reads this mutation as T21994C+del21998_22000, resulting in S:H146del instead of the S:Y144del for normal JN.1*s.
H…
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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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KP.2.2+A22995C(rev), C27382A, T27529C(Orf6:L61I,Orf7a:F46L, S:K478T(rev))
GISAID query: G27382A, T27529C
No. of seqs: 3(Canada 2 USA 1(from India))
First: EPI_ISL_19313873, USA from India, 2024…
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XDV.1.7+T11075C, C28606T(Orf1a:F3604L)+C29370T(N:T366I)+C3885T, C25083T(Orf1a:P1207L,S:A1174V)
GISAID query: C25083T, C29370T,T11075C
No. of seqs: 8(China 7(Hubei, Hong Kong, Heilongjiang), Italy …
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KP.3.3+C25703T(Orf3a:P104L)+T21737C, G29260A(S:F59L)
GISAID query: C25703T, T21737C,G28884C
No. of seqs: 8(Moldova 4 USA 1 Denmark 3)
First: EPI_ISL_19357674, Moldova, 2024-7-3
Latest: EPI_ISL…
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From branch 115 of https://github.com/sars-cov-2-variants/lineage-proposals/issues/1253
JN.1+C23039G, T22928C, C21627A(S:T22N, F456L, Q493E)
Or JN.1.16+C23039G,C21627A(S:T22N,Q493E)
Now usher…
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XDV.1+T13602C+C7564T+A4140G,C23277T(Orf1a:Q1292R,S:T572I)+G20679T,A22994C(S:K478Q)
S:T572I and S:K478Q seems to be a combo pair that appears in multiple branches.
GISAID query: A22994C,A4140G,C…
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