selection analysis of non coding sequences

Question

[vafamayahi]

Hi

I am trying to run selection analysis for non coding sequences using hyphy software. at first the analysis asks for intronic sequence alignment and its phylogenetic tree, but after that the query sequence alignment is needed, which I am not sure about. should the query sequence be an alignment of adjacent gene or not?

has anyone any suggestions what should be uploaded in the query alignment section?

Best,
Vafa