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Hello
I am trying to run treetime mugration on a large dataset. it usually works well on my laptop so far.
I checked the phylogeny and there is no polytomies.
after ~1hrs, it seems to work , GTR.t…
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**Description**
**Sub-lineage of**: AY.112 (classified as B.1.617.2 by Usher)
**Earliest sequence**: 2021/8/23
**Most recent sequence**: 2021/12/20
**Countries circulating**: Israel mainly
**Su…
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**Description**
**Sub-lineage of**: AY.33
**Earliest sequence**: 2021/8/26 (Germany)
**Most recent sequence**: 2021/12/31 (Germany)
**Countries circulating**: Poland, Germany, Spain
**Substitut…
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Hello
I ran treetime mugration and get annotated phylogenies with location states.
I am looking for the equivalent of the getstates function from phytools to summarize/extract the ancestral locatio…
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**Description**
**Sub-lineage of**: AY.4.2.2
**Earliest sequence**: 2021/8/31 (UK-England)
**Most recent sequence**: 2021/1/17 (UK-Scotland)
**Countries circulating**: UK (mainly Scotland)
**Su…
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Issue: as it says on the tin. Most BA.2.38 are called as BA.2 by the latest Nextclade. This can be seen by running on any sample of recent sequences from India, of which a substantial proportion are B…
silcn updated
2 years ago
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First spotted by @corneliusroemer .
**Description**
**Sub-lineage of**: AY.112
**Earliest sequence**: 2021/1/10 (probably some input error)
**Most recent sequence**: 2021/12/16
**Countries circ…
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Sources in Israel told me this potential sublineage started growing in the circulating samples (community, no connection to imported cases) from mid-end November.
**Description**
**Sub-lineage of*…
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As noted first by @shay671 long ago and recently by @bitbyte2015 in #390 and re [highlighted](https://twitter.com/JosetteSchoenma/status/1491808064588156933?s=20&t=IZbs8XsupbLLEjBu8n7HPQ) today by Jos…
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A few people have commented that it could be interesting to incorporate case-count data. I presume we could pull this from Johns Hopkins or OWID? I also assume we'd want a standardizes count as used b…