Dear Elyrajo,

HyPhy does not have a mechanism to set interior nodes to fixed sequences, but you can perform the fit using the hack below, by introducing fictitious terminal branches as in the example below.

Suppose you have the tree

((human,chimp)hca,gorilla,gibbon) and you happen to know the hca sequence.

Then, adding the fictitious terminal branch to 'hca'

(((human,chimp),hca:0),gorilla,gibbon) will have the effect of setting the ancestor of human-chimp to hca.

This hack can be automated, if you have many interior sequences.

Cheers,
Sergei