I want to detect selection signatures on non-coding dataset via HyPhy version 2.2.0 using the similar strategy as proposed by Haygood et al., 2007 Nat Genet. 39(9):1140-4.
The program provides universal codon option and other options which don't seem to be applicable on my dataset. I am at a loss regarding hyphy usage on non-coding dataset as well positive selection using suitable options e.g., 'yangnielsienbranchsite2005.bf' or else? I am in dire need to get this fixed.
is there anybody who can help me in this regard?