Dear Luli,

Your best bet is to do it through the graphical interface. Take a look at the section starting on page 22 of Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login

Other parts of the linked text discuss more about setting up models and parameter constrains.

Cheers,
Sergei

Dear Luli,

I think I understand your objective, but unless I am mistaken, one has to be quite careful about how to remove the clock from a single node (branch). Consider a very simple tree

((human, chimp)hca, gorilla).

You can remove the clock from gorilla and keep the subtree rooted at hca clocklike, but if you remove the clock from human (or chimp), then you can't impose the clock on the rest of tree easily (at least not in the classical sense). Of course you could still have the constraint that chimp+hca = gorilla - is that what you have in mind?

You should be able do this in the interface; simply apply the clock to the entire tree and then un-constrain the branch that you want to be 'free' (select its row in the parameter table and use the eraser button to remove the constrain). This can sometimes fail as well, because HyPhy automatically chooses which branches to constrain and which one to use as free parameters, and your branch of interest may not be constrained. You should be able to get around that by swapping that branch and its sister branch in the tree viewer.

Give that a try and let me know what happens.

Cheers,
Sergei