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I propose to change all instances of 'protein clusters' in our pangenomic workflow with 'gene clusters'.
## Summary of the discussions so far
_I will keep this section up-to-date, the original i…
meren updated
6 years ago
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Hi David,
I am interested in both orthogroups and pairwise orthologs using orthofinder. I have 16 species and get an ortholog results directory for 7 outgroups (0-6). As I understand it orthofinder i…
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Hello,
I was wondering how to get the fasta files for the orthogroups that OrthoFinder finds. In the Statistics_Overall.csv, it reports the number of orthogroups and classify them per number of speci…
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Minor issue with get_count_matrix.py
If there are colons in the SequenceIDs file it can't link it with the sequence IDs in the Orthogroups file.
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Hi folks,
Now that I have the results from Orthofinder. I cannot find the number of genes overlapping and the one to one orthogroups.
Regards,
/SB
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Hi there David,
We've previously ran Orthofinder to calculate to only groups with -oa
`orthofinder -f ExampleData/ -og -t 8 -a 8`
Now we'd like to create alignments of each orthogroup for fu…
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Command call:
```sh
orthofinder \
--from-groups sequences/ \
--only-alignments \
--method msa \
--algthreads 24 \
--msa_program mafft \
--tree_program raxml
```
…
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i think this suggestion is out of the scope of the program, but i'd be a nice addition an option to also cluster paralogs without orthologs.
in most of the cases users are really interested on orthog…
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Hello,
I used orthofinder to cluster orthologous groups from the proteomes of 7 plants and it worked great! I plan to infer gene trees for ~6000 of these OGs. I used trees_for_orthogroups.py to gene…
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Hi there,
We've ran an OrthoFinder analysis wtih the -os option.
However, with the new update, we'd like to give the rest of the pipeline a chance so I've tried running:
`orthofinder -fg $Ort…