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Hello,
I'm running into an error with v 2.5.5: "ERROR: Species tree inference failed / local variable 'speciesTree' referenced before assignment"
I think this might be a similar error to one pre…
emdtr updated
2 months ago
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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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Hello,
Using `N0.tsv`, I'm trying to define the set of single copy orthogroups present in all species. in my case, using 198 bacterial genomes, I get 135 single copy orthogroups. When I check the s…
matrs updated
2 years ago
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Hello! I'm trying to use FASTRAL on an Ubuntu 18.04 machine, but I'm getting an error related to ASTRID and PhyD*:
wirenia@wirenia:~/OrthoFinder-2.4.0/2020-09-15_Sacoglossa/OrthoFinder_results/Result…
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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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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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**Describe the problem concisely**.
Many biological problems are first studied in nonhuman animals, and those cell types are often carefully characterized in e.g. mouse. We would like to take the c…
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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"…