Hi Mike,

Yes, you can fix the branch length -- take a look at Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login

My apologies in advance, HyPhy exposes a lot of the underlying machinery and makes branch length constraints somewhat obtuse.

You can allow negative values for a parameter in HyPhy batch files to remove the (implicitly enforced) 0 lower bound by including the line(s):

Code:

paramaterName :> -1e-25;

 

to reset the lower bound to some (large) negative value.

Sergei