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Hi, I have a query protein sequence and I want to find orthogroup for that sequence. I don't know in howmay species its orthologues are present. How can I run orthogroup for it. What I understood from…
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Good Afternoon.
Orthofinder team.
I have run the Orthofinder (./orthofinder -f mydata) process with 1000 proteomes of different bacteria species, After some days, I had some erros in order to gene…
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Similar to the issue posted in #58. I have tried removing any orthogroups where a gene only occurs in one species, and I've also tried a more extreme case where I removed a group if any species did no…
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https://github.com/AndersenLab/Caeno_Scan/blob/33b84ea916297fd693a0be5e460c1f0634fc1ed1/multi_species_simfiles.nf#L73
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Hello!
I tried to run compare_genomes on several species, got an error
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Error in file(file, "r") : cannot open the connection
Calls: read.nexus -> scan -> file
In addition: Warning mes…
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Hey,
Many people are asking about orthogroup annotation (https://github.com/davidemms/OrthoFinder/issues/373 , https://github.com/davidemms/OrthoFinder/issues/411 , https://github.com/davidemms/Ort…
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I'm working on a project where I get data in series. For each round, I use OrthoFinder which works great and the output is extremely intuitive but takes a long time and uses a lot of compute power.
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Hi, I am missing the scripts for creating the plots in figure 2 and the scripts to generate the relevant data. I am missing the same for parts d and e of figure 3. Could they please be added or shared
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Hello,
Thanks for developing such useful tools. I want to use AGORA with providing the orthologous groups files and not the trees; I have a question regarding these orthology groups. I used Orthofi…
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The txt file has more orthogroups that the csv file (there are more in the former). Is there a reason for this? I checked the orthogroup gene count file and it matches the counts in the csv file.