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?
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.