Hi
I have an alignment of ~30 sequences of 4kb where the most interesting part is a 60 bp region where i have recorded  7 InDel events so the region looks like this:
xxx-----xxxx
xxxx--xxxxx
xx--xxxxxxx
x-----------x
xxxxxxxxxx
Is there a way to test the hypothesis that this region is under positive selection? like testing whether a tree generated in this region is different from a tree of neutral sites in the rest of the gene? is there  a way to tell HYPHY do consider gaps?
thank you
Hanan