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**Description**
Sub-lineage of: BM.2
Earliest sequence: 2022-9-11, Australia, Australian Capital Territory — EPI_ISL_15477002
Most recent sequence: 2022-9-23, Australia, Australian Capital Territor…
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Hi!
I have a quick question regarding the generations assumptions of the skyline analysis. In the output (to the screen and in the skyline.tsv file) the program assumes 50 generations per year. I …
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Hi there
I have installed treetime on windows 11 using:
git clone https://github.com/neherlab/treetime.git
cd treetime
pip install .
I get the message:
Successfully installed phylo-treetime-…
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Currently hitting https://github.com/neherlab/treetime/issues/169 which I don't think I noticed previously, but no change to treetime codebase so probably I was hitting it without noticing and need to…
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### Current Behavior
After migration of neherlab, when I try to upload using `nextstrain remote upload https://nextstrain.org/groups...` the upload fails and I get the following uncaught Python error…
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### Current Behavior
`Error: The connection to the remote server was severed before the upload finished.`
### Expected behavior
Upload works or I get a meaningful/helpful error message with suffi…
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Hi,
We are subclassing Bio.Align.MultipleSeqAlignment in our project but when we use an object of our class to do root-to-tip regression using timetree it raises a MissingDataError at line 186 in s…
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Some BE.9s sequences are being designated as BA.5.3.1, probably due to a 244 nt deletion in ORF7a (position 27508-27751) which were not reported in the original BE.9 sequence.
Here is an example in…
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I noticed a difference in behaviour when reconstructing using vcf or a fasta alignment for ambiguous bases. In the resulting nexus the ambiguous bases in samples are labelled as changes to reference i…
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Hello,
I am trying to download the arrays of pairs of SNPs for each individual. Whenever I click one of the links to download the p6 cocounts I get a 404 Not Found message. For example, the URL I am …