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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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TreeTime flags leaves that do not conform to the clock model like so:
```
263.56 TreeTime: The following tips don't fit the clock model, please remove
them from the tree. Their dates have …
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Some possible enhancements to interface:
* ~~toggle between by-country and by-clade views - I think currently user has to go up one level to do this~~ there is not a one-to-one map between views (reg…
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*************edited November 20***************
**TRACKER**
BA.2.86: -C6541T,A7842, C8293T, G8393A (new query thx to @aviczhl2 )
JN.1 QUERY: C18894T, T15756A, A7842, -C6541T
XDD Query : C6541T…
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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 …
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**Description**
**Sub-lineage of:** BA.2
**Earliest sequence:** 2023-7-24, Denmark
**Most recent sequence:** 2023-7-31; Denmark & Israel
**Countries circulating:** Denmark (2), Israel
**Number of…
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* Fairly naive build environment running Ubuntu 20.04.6, *i.e.*, no `npm` or `snakemake`
* cloned repo with `git clone https://github.com/neherlab/flu_frequencies.git`
* checked out `web` branch (wa…