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Hi,
When I try to launch the clade_refinement step I get this error message like the project identifier does not exist:
`./ham_art.pl clade_refinement sample_001,sample_002,sample_003,sample_00…
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Hi Benoit,
I am implementing a parse for GeneRax output, and specifically the reconciled tree in NHX format as that's how they come out of the program with the `--reconciliation-samples` option.
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flass updated
4 years ago
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• Ideally, there would be a specifiers & qualifier box that is specific to each definition type (for example, so that using an apomorphy as a specifier is not possible if the definition type is minimu…
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Hi ! When I check cafetutorial_clade_and_size_filter.py at https://iu.app.box.com/v/cafetutorial-files/folder/22161186238?page=1 , I found the script will write out wrong gene families with only one g…
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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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[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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The CalibratedYule method accepts one or more clade taxa with their given mrca age and generates a tip-labelled time tree. If a root age is provided, the method conditions the tree generation on this …
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1. Use the clade classification logic to expose an api for users where they can submit their sequence and get the predicted clade along with the accuracy, precision score, etc. for the prediction made…
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Hi,
I have a problem plotting clade labels. They seem to oriented inverted, if I plot them using `angle = "auto"`
```
> library(ggtree)
> library(ape)
> x p p rotate_tree(p, 90)
Coordinat…
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### Context
`augur clades` currently places clades by finding the biggest branches on a tree that satisfy each clades defining mutations as provided by the user.
This method has a few downsides:…