Question: How can I extract paralogs and orthologs seperately from Orthofinder output?
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gravatar for mirza
3.7 years ago by
mirza120
India
mirza120 wrote:

Hi, I am using Orthofinder and got an extensive output with orthologs and paralogs arranged in different orthogroups. My question is how can I extract the paralogs and orthologs seperately from the orthologs.csv output file?

ADD COMMENTlink modified 2.8 years ago by david_emms110 • written 3.7 years ago by mirza120
2
gravatar for david_emms
2.8 years ago by
david_emms110
david_emms110 wrote:

Hi

In case anyone else has this question.... the current versions of OrthoFinder now produce files of orthologues between each species pair that it infers by analysing the gene trees.

If you also want to specifically find paralogous genes then these are the genes in the Orthogroup.csv file that aren't in the orthologues file. The GitHub page has a nice explanation of orthogroups v orthologues v paralogues.

All the best

David

ADD COMMENTlink written 2.8 years ago by david_emms110

How do you retrieve the paralogs out of the Orthogroup.csv file?

ADD REPLYlink written 2.2 years ago by hudak70
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