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Hi, I am using Biopython 1.79.
Sorry, I admit this is a detail, but I reference it in case comment parsing is updated in the future. I could participate in that.
### Expected behaviour
Commen…
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How it might work:
1. Get taxonomic information from the database in a kingdom/phylum/class/order/family/genus table format. This could be done via templating (slow) or ajax (more complicated?).
2. Tu…
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For my SARS-CoV-2 Nextclade trees I make extensive use of constraint trees (see e.g. previous issues #102, #144, . The following are some thoughts on making constraint tree validation throw a more hel…
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Currently, I have the following setup:
`gene_tree = read(gene_tree_fp, format='newick', into=TreeNode)`
I would like to return the Newick string representation of the gene_tree but without the dista…
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I am trying to upload and analyze data in newick format, but the uploading process seems to never finish. It is the same with sample newick files. There is no problem uploading the files to other loca…
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I ran Orthofinder.
Best outgroup(s) for species tree
---------------------------------
2022-11-28 16:11:52 : Starting STRIDE
Traceback (most recent call last):
File "/home/olivia/anaconda3/en…
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Hi @michaelmiyagi ,
I've finished the test of QuIBL and everything was okay. However, I got this error when I tried to run the script using my own tree file as below:
nohup: ignoring input
Traceb…
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Hi,
I have been using CAGEE to look at gene expression across mammalian species across 9 tissue types. I have installed and am using the beta version of CAGEE : CAGEE1.1.1.beta
I have previousl…
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Hi,
I have used PanX successfully a few month ago. Now that i have migrated on ubuntu 18.04, i tried to reinstall it via git clone then conda install, but i failed to run the test... Here is the erro…
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```
The newick exportation feature seems not to respect rotations that were
manually imposed within the program.
For example, in the attached dummy files, a.nexus and b.nexus differ by a
rotation.
B…