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Hello,
I notice that you did phylogenetic trees in CITUP with the output from PyClone.
However, In my work, run_analysis_pipeline commands can't give an output of mutations which didn't appear in …
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Update code for making phylogenetic trees via `gdtools PHYLOGENY` and then generating graphics. This would be useful specifically for adding to the LTEE-Ecoli website.
https://github.com/barricklab…
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I was able to drag and drop my output files from RAxML and roary; however I have not been able to find a way to root my phylogenetic tree at the outgroup branch in Phandango.
Is there a way to root…
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Greetings -
I've started 4 phylogenetic trees in the morning today, Feb 24th (10 hours ago) . One of them worked well and fast, but 3 others are not done still. Is it possible to find out why they …
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I think it would be valuable to create a phylogenetic tree sub workflow.
1. autoMLST-based tree
2. GTDB tree using [de_novo_wf](https://ecogenomics.github.io/GTDBTk/commands/de_novo_wf.html)
3. …
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- Klaus Schliep (UMass Boston)
- https://CRAN.R-project.org/package=phangorn (GPL 2.0 or greater)
development version: https://github.com/KlausVigo/phangorn
- The R package phangorn contains met…
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### Theory
- Tidyverse
- Pipe
- Visualisation
- Rmarkdown
### Practice
- Phylogenetic trees
- Genome structure
- ORFans
- patchwork
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dear author,
i wanna visualize the result of r8s, which is a program for analysis of rates of evolution.
Fortunately, i found the ggtree package that could realize it. but when i use it, something…
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Create function that calculates RF distances between 2 phylogenetic trees.
You will need to read slides 55-58 and 60 from merged lectures posted by me on slack and details from https://rdrr.io/cran/a…
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Hey, Daniel! I use a tool called [Taxonium](https://taxonium.org/) to visualize phylogenetic trees. It seems like Taxonium has a [React component](https://docs.taxonium.org/en/latest/component.html); …