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Dear TracerX team :
I'd like to thank you for creating CONIPHER, it has been immensely useful in my work. I've been working with constructing tumour phylogenetic trees and came across an issue that …
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I'm the creator of nxviz, and would love to see some of your code in our codebase! In particular, I'm looking for declarative ways of making CircosPlots, ArcPlots and others. Would you be open to work…
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I tried to include a markdown table in the description of this dataset: https://www.openml.org/search?type=data&sort=runs&id=45081&status=active
But it does not seem to render:
Both the Gith…
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I tried running `alt_frac` and `coverage` scoring methods on the same inputs. Then I calculated the VAF based on alt and ref reads from the `coverage` output matrices. Most of the values agree, but so…
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Dear Pargenes,
Is there a feature in Pargenes that allows you to sort trees by the number of taxa in each tree?
For example, most clustering programs will output single copy core gene alignmen…
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Hi all,
I am trying to use the feature of phylogeny in wndchrm, but it is not working. Following are the steps, which I have tried in Ubuntu:
First, install packages:
sudo apt-get install ph…
ghost updated
7 years ago
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Hello,
I really like this fantastic program to draw Cafe output files. When I used it with my data, the numbers of significantly expanded and contracted families are the same while the example data…
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Hi! I was using GCTree for the inference of phylogenetics based on sequence number of about 1000, it is super slow. Do you have any optimization on that?
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Hi David,
Thank you a ton for developing and maintaining OrthoFinder and various related software! They have been instrumental in my research.
Perhaps something you are already aware of, but I noti…
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Hello,
I am wondering if there is a way to draw scaled trees and simultaneously reduce the size of the labels. Any guidance on this would be greatly appreciated.
```
import tanglegram a…