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## The problem
TreeTime has currently a very rudimentary way of resolving polytomies (multi-furcations in the tree).
When this was initially put in place it was never meant to resolve large polyt…
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Hello,
On the roary website it mentions that panx can be used to visualize the data. I'm trying to load data into panx like the panx website says but the roary output is not recognized. I'm follo…
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Hello Richard,
Since there is no relaxed clock argument in "rule refine" in Augur, I have tried to separately run Treetime with --relax argument then put the results back to the pipeline as they're…
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replace the current alignment algorithm with something that tolerates gaps
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In order to perform refactoring and to add new features with more confidence, we need unit, integration and end-to-end tests for:
* algorithm parts. See`src/algorithms`
* React parts - compone…
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Hi!
First of all, thank you for putting together such a nice pipeline! It's very convenient to have all of these tools in one place.
I installed BEAV using conda as per instruction on the readme…
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I'm running this code and run into an index error:
treetime --tree /Users/ouotodou/Desktop/treeee.nex --dates /Users/ouotodou/Desktop/sampled_metadata.csv --aln /Users/ouotodou/Desktop/sampled_seq…
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Hi,
I started using treetime recently and some of my trees look like this, while the others look fine. My sample size is 25 and here is an example code that I used.
`treetime --tree VREst18_clonalfr…
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# 🙋 Feature Request
## 🔦 Context
Continuation of #660 and #669
## 😯 Describe the feature
We don't have a strict TODO here, so some imagination is required :)
But here are…
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Probably a simple approach to visually compare the backbones of the Viridian UShER tree and our pandemic-scale ARG is to leverage the Pango lineage roots, excluding the Pango recombinants. The Pango l…
szhan updated
1 month ago