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Is there a specific interpretation I should make if a gene is assigned to an orthogroup, but it does not appear it in a HOG? I've tried looking through the documentation, but I don't see much about HO…
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Hi David,
Thanks so much for this very valuable resource!
Because N0.tsv "effectively replaces the orthogroups in Orthogroups/Orthogroups.tsv" I suggest to update the Comparative_Genomics_Statisti…
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Hi!
I wrote a [quick-and-dirty script (`orthogroup_to_gene_name.py`)](https://github.com/MrTomRod/orthofinder-tools) that takes `Orthogroups.tsv` and turns it into `Orthogroup_BestNames.tsv`. This …
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Dear David,
I would like to produce an Orthoxml output file from my analysis, and everything goes well until building the file. The data I use are private so not on an online database, could that …
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Hello!
I am trying to run PosiGene and think it's great!
We know the OrthoMCL format is the output of arguably the most popular homology prediction software and of several databases of predic…
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Hey David
It just came to me that there might be a better nomenclature for the HOGs, since they are hierarchical.
Would it not be possible to have a [EC-numbers](https://www.wikiwand.com/en/Enzy…
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When I execute the orthofinder-2.5.5 program,en error was occured. And the outputs are list below, how can i deal with it. anyone can give me a help please?
OrthoFinder version 2.5.5 Copyright (C) …
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I tried running cafe5 with many species and got a valid lambda only after removing 17 OGs (from orthofinder). However, afterwards I always get the following error:
```
Filtering families not prese…
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Hi:
I'm trying to convert the species tree to ultrameric to use in CAFE, so I would like to know which of the trees (rooted or rooted _node_labels.txt) is best to use.
However, I have this issue:
…
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Hello again,
I am running 90 days now Orthofinder for 30 species. Yesterday my job killed in the gene constuction step (raxm-ng).
So, is there any solution to rerun orthofinder again from this st…