I have exons from a reference taxon. I want to now identify putative homologs from transcriptomes of 5 other species using the reference exons and reciprocal best hits BLAST. I've seen a number of threads and scripts that primarily focus on performing RBH with two species only, and I realize this is what RBH does in the background. However, I'd like to do this across all species so I know not only what is a putative homolog between species 1 and reference species, but between species 2–5.
The idea is that I can then extract exons that are identified across all species, or alternativley, that are found in at least two species to create a variety of datasets. Is anyone aware of any scripts that can do what I'm needing done?