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### Context
I've tried to get `treetime` included in the list of tools that should have consistent versions across docker builds.
The reasoning is that `treetime` is a core Nextstrain component th…
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Hi,
I'm running TreeTime 0.11.2. There should probably be a check in `TreeTime.clock_filter` that checks the value of `method`:
```python
if method != 'residual' or method != 'local':
rais…
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There seems to be a regression for feature #444 in that the accessions are downloaded rather than opened in new file.
This is probably because there's no longer a `downloadAsFile=false` URL paramet…
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The old Nextstrain integration was removed in #264.
![image](https://user-images.githubusercontent.com/18666552/137744248-c28b7a25-5828-446f-b87b-344da6e97928.png)
It only supported Switzerland …
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I've noticed that the proportion of `BA.2* + S:452R, S:486V, S:493.` in South Africa (and elsewhere) has been rising recently.
These should really be BA.4/5 but are misassigned, either by pangoLEAR…
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I've received a request for Avian flu datasets e.g. H5, via Twitter DM.
If you'd like this feature, feel free to leave a thumbs up here to signal support.
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### Current Behavior
Given a site with a reference allele and a N (encoded in a VCF file), then that site is not included in the output JSON or the output VCF. This is expected behaviour unless we …
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Hi,
I'm going to use treetime but I run out with this ERROR:
Attempting to parse dates...
Traceback (most recent call last):
File "/root/anaconda3/bin/treetime", line 8, in
sys.exit(…
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The current "tile" UI to navigate to datasets on the splash page works for well for a few items; it's attractive and approachable. However, I can imagine aiming for ~20 core datasets alongside as abou…
trvrb updated
4 months ago
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### Context
I run some nextstrain builds for the neherlab group on a cluster in a cronjob and they work reliably. The one thing that makes them fail is expiry of `nextstrain login` refresh tokens eve…