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Hello,
I am trying to run orthofinder. Here is my command:
`orthofinder.py -f . -t 64 -M msa -A mafft -T fasttree`
and here is the output:
```
OrthoFinder version 2.5.4 Copyright (C) 2014 Da…
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Hi Agora-team,
I have been trying to learn how to construct ancestral genome karyotype for ever, and was never been able to understand it properly and then saw your paper and I was like wow. It is …
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I have used orthofiller and have following issues:
1. "0.1. Checking installed programs" failed to test some shell commands
I'm sure that I have these shell commands but this step somewhat failed. S…
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Hello,
I was wondering if there was an alignment file for the orthologues hidden within the results folder.
Also, is there a way to add the species name to each header of the orthologues fast…
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Hi David,
I am using Orthofinder 2.5.4 on a dataset of 15 organisms. My output states, "There were 2989 orthogroups with all species present and 30 of these consisted entirely of single-copy genes"…
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**A suggested workflow**:
A common request is be able to run OrthoFinder using IQTREE. This can create problems for most users because IQTREE can use a lot of RAM and so running multiple instances in…
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Dear Davide
When I use orthofinder, I come across a strange problem
Traceback (most recent call last):
File "orthofinder.py", line 7, in
File "scripts_of/__main__.py", line 1765, in main
F…
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Hi,
Thank you for sharing your cafe pipeline. However, I ran into the following problems:
```
> awk -F'\t' '{print "(null)\t"$0}' Orthogroups.GeneCount.tsv > tmp.tsv
> sed -i.bak 's|(null)|Desc|…
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Hi David,
Thank you for developing this software. I would really appreciate your help if you could clarify my following doubts:
When I use orthofinder to analyze 47 samples about 40 species of RNA-s…
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Our cluster has a new policy of allowing only a million files per user, and I'm feeling this limit with a few Orthofinder runs - there are tens of thousands of files in the Orthogroup_Sequences, Resol…