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Hello, first- time issue report here, so I hope I'm not making mistakes while reporting.
I've tried following the example of fitting a proportional random error effect structure here: https://cran.…
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Hello!
I observe that during the execution of the program iqtree2 in compare_genomes, the parameter ‘’-o‘’ for specifying the outer class group is not included. Whether an alternative option should…
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Dendropy seems to be really slow when working with the supertrees, if it is even working at all. I need to find a faster way to work with the supertrees that will let me check the list of taxa agains…
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**Submitting author:** @DamianJM (Damian John Magill)
**Repository:** https://github.com/DamianJM/T-REX
**Branch with paper.md** (empty if default branch): main
**Version:** v1.2
**Editor:** Pending
*…
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Dear Daliang Ning
You developed a very good R package, but I encountered some doubts in the specific application. Based on the sample data you provided, in the result folder TestOutputs, I did not f…
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Hi,
Trying to use gemelli as a qiime2 plugin and I get the following error:
```
/home/sdegregori/miniconda3/envs/qiime2-2023.7/lib/python3.8/site-packages/gemelli/preprocessing.py:423: RuntimeW…
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# Scope
Computational paleontology (or paleobiology) is a thriving field. Gone are the days of just digging up fossils; paleontologists now have the luxury of being able to perform a wide array of co…
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I'm trying to create a custom RSV nextclade dataset following the tutorials from https://docs.nextstrain.org/en/latest/tutorials/creating-a-phylogenetic-workflow.html#annotate-the-phylogeny and https:…
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I am trying to make phylogenetic tree using binary data. I tried using grapetree -p MGE_binary.txt -m MSTreeV2 >out.phy. Please suggest.
Example Input file:
C1 C3 C5 D1
gene1 …
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**Describe the bug**
When the levels of a categorical moderator are not capitalised to begin with, orchard_plot() breaks with changes to 'upper' or 'tree.order' options. Below I demonstrate with a re…