I have sequence data for a set of immune genes from several individuals from several populations. I would like to test for patterns of selection within each gene.
Is there a way to do this?
I was thinking of running tests in FUBAR and MEME, but I am unsure if I need to include outgroup(s) in these tests?
Is it possible to take an alignment of e.g. 10 sequences (I know this is a low sample size, but it is what I have) for each of three populations for a given gene and run selection tests on this?
Thank you very much for any advice! Hjalte