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## New lineage proposal
by Michael K. Edwards
### Description
Sub-lineage of: B.1.1.317
Earliest sequence: collected 2020-11-17
Most recent sequence: common in Russia and Poland (as of mid-Apr…
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Hello TreeTime team,
I am getting a Newick formatting error when running TreeTime with a large dataset. The tree contains 195,351 SARS-CoV-2 sequences, was built using FastTree, and does contain …
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BA.2.86
Branches (more than 1seq only):
**1 = BA.2.86.1 = Orf1a:K1973R (A6183G), C12815T query :A6183G, C12815T**
1a : Orf1a:Y621C (A2127G) Query : A6183G, C12815T, A2127G
1a1: G2527A, ORF1a:P…
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I would like to ask you to use nextclade better.
I want to analyze new pathogens that do not correspond to the species provided by nextclade (covid, mpox, etc.) using nextclade. I understand that a…
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Left this on the associated PR without realizing it was PR.
https://github.com/neherlab/treetime/pull/205
[hcov-229e.zip](https://github.com/neherlab/treetime/files/11807773/hcov-229e.zip)
I…
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For the development of the "viewing" frontend (e.g., https://github.com/pathoplexus/Planning/issues/80), we need a dataset that contains different versions. Ideally, the dataset would have a column `r…
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When running` treetime 0.10.0 ` with the following command:
`/home1/jh212a/.local/bin/treetime --aln /home5/nCov/Joseph/Phylogeny/GISAID_1Feb2023/analysis/alignment/Scotland89220_greatancestoralign…
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You already upload raw fasta to AWS in `rule upload_sequences`.
It would be useful for our repo to be able to download metadata.tsv as produced by your `rule parse`.
I will duplicate your parse for…
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**Current Behavior**
For some datasets or zoom levels, the downloaded per-strain metadata is a file with one line:
```
strain
```
**Expected behavior**
The downloaded metadata should re…
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On apparently OK data, treetime 0.10.0 (master) throws `IndexError: index 0 is out of bounds for axis 0 with size 0` when run as part of `augur refine` in `--use-fft` mode:
```bash
❯ augur refine …