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Hi! I noticed that the version `2.0.0` has recently been released and upgraded this to a static application. All local server components were removed. However I cannot find the documentation for this …
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Seeing this error from `augur refine` in our private seasonal flu builds:
```
[batch] [2023-04-20T15:51:14-07:00] Traceback (most recent call last):
[batch] [2023-04-20T15:51:14-07:00] File "/usr…
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### Command description
Makes timetrees of phylogenetic trees, used in genomic epidemiology of e.g. SARS-CoV-2, monkeypox, flu etc.
### Command details
0.9.4
### OS
- [ ] Android
- [X] Linux
- [X…
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### Current Behavior
The help text of `--year-bounds` states:
```
--year-bounds YEAR_BOUNDS [YEAR_BOUNDS ...]
specify min or max & min prediction bounds for samples w…
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_What I have done so far with the pangenome pipeline?_
I created all the pangenomes using your PanX pipeline but I am unable to visualize the results.
- I have a fresh install of both the pan-ge…
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This code fragment generates an index error if there is a mutation entry for the last sequence position as it does not check before using index `pi+1`
https://github.com/neherlab/treetime/blob/a27c…
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It seems that Nextclade web may not necessarily get faster after a certain number of threads is reached.
In particular, it may even get slower, as the setup time seems to increase with the number o…
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**Current Behavior**
About every 10-20min browsing Auspice trees with ~3000-4000 genomes my whole Brave browser will hang infinitely when I zoom into a branch. This doesn't happen on every branch c…
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Hi,
I am still trying to use tools in the augur package to clock trees produced by the UShER package. Previously I had encountered some unexpected errors related to subtrees with extremely long bran…
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### **Description**
**Sub-lineage of:** BQ.1.1
**Earliest sequence:** 2022-12-9, Australian Capital Territory — EPI_ISL_16359648
**Most recent sequence:** 2022-12-15, Australian Capital Territory —…