I'm currently trying to find candidate genes related to a certain pathway of my species of interest. My approach began by screening certain gene families after performing DGE on some datasets. After obtaining my initial candidates I want to compare them with other genes (from the same family) involved in similar reaction/roles.
My question is regarding the use of an outgroup sequence in this analysis. My understanding is that an outgroup should be a sequence (or sequences) that are outside the group of interest and more distantly related to the ingroup. So, since I'm studying a gene family and not orthologs genes I'm not sure If I should include a sequence from the same family but outside my taxa. Does this make sense and is there anything I should take into consideration while analysing my results?
Thanks in advance