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Dear RERcoverge designer,
I'm running into an error when I try to run RERconverge with my data.
When I run the getAllResiduals with the built tree, the results are all NA.
![image](https://gith…
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Hi, I'm working with a dataset where many genes have duplicates. I'm feeding in a master species tree to serve as the 'background', but it seems like the RERconverge expects to only have one gene per …
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Hi,
I have read many related issues, but I'm still confused. From OrthoFinder, I can get a file including all OG.fasta. The single-copy orthologs are no problem, but for the multi-copy fasta files,…
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I am running an ASTRAL analysis on 60 gene trees generated from 60 plastid genes for ~5000 taxa. In the final ASTRAL output tree, the bootstrap support value is the same for all terminal branches. Wha…
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Hello,
When running QuIBL, I encounter a "ValueError: math domain error" after the program runs for quite some time. I've tried two different data set sizes (16801 trees, 7645 trees). I've also var…
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Dear Cai,
I want to use your scripts to test my data. I used python 3 and R v. 4. I have installed all the packages your scripts suggested.
However, when I use the following command to run…
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Hi,
I want to run OrthoFinder from the Gene Trees step onwards. The reason is that I am only interested in the duplication history of a subset of orthogroups. However the default of OrthoFinder is …
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Hello there, thank you for this really great tool.
Lately, I am trying to perform an orthofinder analysis using 38 species as input, but I am having the following problem.
After the diamond anal…
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Hello,
weightMat
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Dear @BenoitMorel ,
Thanks for creating such a great program. I'm really interested to see how it performs on our data relative to other software (e.g. astral, astrid). Asteroid seems to have no is…