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**Current Behavior**
When I select "color by">"Genotype" and then start entering a list of sites, e.g. select "S" then `95,142` Auspice becomes sluggish as soon as I've typed the first comma. Auspi…
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Dear Devs,
I hope that you are well.
I am using TreeTime (v 0.11.3), installed with `conda install bioconda::treetime`.
I am using the ancestral sequence reconstruction (with VCF files) comma…
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There's a number of datasets that could be helpful with this effort. In order to most effectively keep track of them we should establish a documentation method. This could be a Google Doc or Sheet, a …
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Hi,
I am planning to run multiple scenarios based on the distribution of input parameters. The idea is to understand the contribution of each parameter individually on the trajectory of the disease…
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### Current Behavior
Running augur refine in the monkeypox build we get the following error:
`ValueError: x and y arrays must have at least 2 entries`
### Expected behavior
No error
### How t…
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$ augur refine \
--tree results/tree_raw.nwk \
--alignment results/aligned.fasta \
--metadata data/metadata.tsv \
--output-tree results/tree.nwk \
--output-node-data results/branch_leng…
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@madhasri
**Paper on Seasonality:**
Potential impact of seasonal forcing on a SARS-CoV-2 pandemic
View ORCID ProfileRichard A Neher, View ORCID ProfileRobert Dyrdak, View ORCID ProfileValentin…
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I got this error from refine that I struggled to debug:
```
$ augur refine --tree builds/tree_raw.nwk --alignment test.fasta --output-tree builds/tree.nwk
...
ERROR: SequenceData: loading alignme…
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Hello
I am teaching myself how to run panX using TestSet. Here is the command I run exactly following the instructions.
./panX.py -fn data/TestSet/ -sl TestSet -t 32 > TestSet.log 2> TestSet.err
…
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**Context**
As I'm writing the weekly situation reports, it would be a *huge* help to be able to deep link to a view of the tree that's zoomed into any arbitrary node, rather than having to define …