If I try to cut and paste into the "Enter command" box under likelihood in parameters not only does it not work but it then prevents the clipboard working with any program until I shut HyPhy down. Is there any way to stop this happening? I'm trying to cut and paste the replicate constraint command on page 58 of "Estimating selection pressures on alignments of
coding sequences" and I haven't been able to get it to work by typing it in manually.

And I've now got replicate constraint to work. In case anyone else has this problem the following code works:


global R=1;ReplicateConstraint ("this1.?.nonSynRate:=R*this2.?.synRate", MammalsBirds_tree, MammalsBirds_tree);