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[In the phytools package there is an option to plot clade names as an arc using the arc.cladelabels function](http://blog.phytools.org/2017/05/arccladelabels-using-names-of.html).
```{r}
library(a…
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There are three types of content that will probably remain in this repository:
1. The components of the Clade Ontology as individual PHYX files in JSON.
2. The scripts that generate and test the C…
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root@634f60c5aa0a:/data# biobakery_workflows wmgx --input S10 --output S10_OUTPUT
(Nov 13 06:45:17) [ 0/44 - 0.00%] **Ready ** Task 0: kneaddata____D1-1_combined_R1
(Nov 13 06:45:17) [ 0/44 - …
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The homepage now includes a nice tree showing the relationship between the variants.
It would be nice if a user could click on the circular nodes or text labels to navigate to the corresponding var…
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### Context
In RSV I would like the root to belong to a clade so that any descendants that are not part of any other clade get that clade.
I'm not sure this is possible right now - it's relevant b…
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Hi @jhpoelen
As we talked the ideia is to implement a fuzzy match in nomer.
Here an example from GlobalNames
`echo -e "\tHomo sapens" | nomer append globalnames`
Output:
```tsv
Homo sape…
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```
> classification("predict_pmv-95", db = "ncbi")
== 1 queries ===============
Retrieving data for taxon 'predict_pmv-95'
√ Found: predict_pmv-95
== Results =================
* Tot…
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We will typically just need to get clade assignments (and summarize to counts of clade assignments) for samples that were collected within a particular date range. We should be able to specify those …
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The annotation DB will contain many different targets, and it would be interesting to be able to easily see / query those definitions. This could also potentially lead to re-use of definitions for the…