DataSetFilter filter1 = (...);
DataSetFilter filter2 = (...);

define model, tree string here...

Tree T1 = treeString;
Tree T2 = treeString; /* same topologies */

ReplicateConstraint ("this1.?.?:=this2.?.?", T2, T1);
/* this will constrain all LOCAL (i.e. branch length
parameters in T2 to be the same as their counterparts
in T1, assuming the same model is applied to both trees.
If different models apply, additional steps are needed,
to scale parameters appropriately.
Look in messages.log to see what constraints have been
generated. */

LikelihoodFunction lf = (filter1, T1, filter2, T2);
Optimize (MLEs, lf);

etc...