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When running snakefmt on the following rule the `alpha` and `line_style` declarations are intended for no reason.
This breaks the code obviously. No idea what could trigger this behaviour.
Is …
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Hi Ziheng, Tomas -
Forgive me for asking such a dumb question but I am simply trying to understand the posterior branch lengths (taus) and relate these (roughly) to standard genetic distances. My u…
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Hello,
In the radius search CPU, you are using:
```
tree = scipy.spatial.cKDTree(x.detach().numpy())
_, col = tree.query( y.detach().numpy(), k=max_num_neighbors, distance_upper_bound=r + 1e-8)
…
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Currently the formatting of the help messages (defined via the leading docstrings at the start of each script in `augur/*.py`) is not respected by `augur --help`. We should improve this which will en…
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Hello there,
I don't seem to be able to get a .dnd output when running mashtree from *msh files, whereas I can get a .dnd output if I run mashtree using the fastq files as input... see below
I ra…
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I have test the algorithm on my dataset , the distance height is between 0,1. for example it assign 0, 0, 0 , 0 then the rest are 1.
the distance is a matrix from euclidean distance method …
ghost updated
4 years ago
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I'm currently going through the source and I'm having trouble to understand how interval tree `A` is updated in [`ForwardUpdate`](https://github.com/twitter/BreakoutDetection/blob/master/src/edmTail.c…
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### Describe the workflow you want to enable
#### Graph-Based Clustering ([original repo link](https://github.com/dayyass/graph-based-clustering))
**Graph-Based Clustering** using connected comp…
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@pierre-lebodic had the idea to measure distances between leaves, to know whether part of the tree is over/under represented. Can you concretize this further?
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Hi @lucblassel,
I want to calculate Unifrac distance (https://en.wikipedia.org/wiki/UniFrac) in parallel for a very large tree (3,000,000 tips), this is related to compute sum of branch length of s…