I have 3 species A, B, C and tried to use orthofinder to find the genes existed in A B species but absent in C species. Then I got the results from orthofinder, there is about 19691 OG number (gene families) existed in A, B species but absent in C species, I think it is too much? but not sure what's wrong with it ..
Then I tried to only use A, C species for orthofinder, and find genes existed in A species but absent in C, the results only have 23 OG number, ( if I tried B, C species, the results is also only 32 OG number), much less than the results when we put A, B, C together.
So I am quite confused why this happen and not sure is the results is realiable..any suggestions will be pretty appreciated!