I am trying to set the initial parameter guesses because I think HYPHY is starting with very bad values. My model defines a different parameter t for every branch. So I am trying to set the initial values using commands like:

tree.Node5.t = 1.0;

However, when I look at the messages.log file, it doesn't seem that these initial values are being used. Instead it says things like:

Initial guess for tree.Node5.t is -863064

How do I set the initial guesses so that they are used?