Conserved Regulatory Sequence In A Subtree

Question

[Asaf]

Hi Biostars I'm trying to find out to what level on a phylogenetic tree a regulatory sequence is conserved. I take known regulatory sites from E. coli and try to find where this region was gained in evolution. My question is how do I do it in an elegant way rather than just extracting the sequences, deciding which are similar enough to the one of E. coli and reconstructing the event on the tree to get the gain node. I found the program dless from phastCons that should do that but this program finds a conserved sequence that was gained not necessarily in my clade of interest. Do you have any idea? Thanks!

Answer 1

[Asaf]

I found a solution! I thought of using phyloP from the same package with the subtree option and test all ancestors of E. coli with the LRT model, then choose the ancestor that gives the highest likelihood ratio, since the null hypothesis is the same for all of the subtrees, this is the subtree with the largest likelihood.