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Proposal for a sublineage of BA.2.3
Earliest sequence: 20.08.2022 (Indonesia)
Countries detected: Indonesia (1)
I noticed a strange sequence uploaded today from Indonesia (**EPI_ISL_15005560**) c…
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## The problem
TreeTime is (up to polytomy resolution) a method that scales linearly in tree size, but some steps are slow.
This is partly due to the fact that its in python, partly due to suboptim…
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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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When looking up why @anna-parker's branch CI checks failed, I noticed we seem to have insufficient credit to run Travis CI builds making it look like commits failed.
https://app.travis-ci.com/githu…
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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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I keep getting the error below. Any clue?
treetime homoplasy --aln homoplasy_25807.fna --tree Multifasta_25807_aligned_.nwk --verbose 6
0.00 -TreeAnc: set-up
read alignment from file homoplasy_25…
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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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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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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…