When I do a relative rate test, hyphy gives me constrained and unconstrained results.  For my constrained results, I expect the rates of the two ingroups to be identical (constrained to each other), but they are not. Why is this, and how can I fix this?  My current inputs are :

["00"] = "Codon";
["01"] = "Universal";
filename
outgroup
["04"] = "GY94";
["05"] = "Local";
["06"] = "nonSynRate

My output is:

_________________RESULTS_________________

Full Model Results:
Log Likelihood = -1949.89403756304;
Shared Parameters:
kappa=0.289971

Tree threeTaxaTree=(Ingroup1:0.0124459,Ingroup2:0.0228679,OutGroup:0.229406);


Constrained Model Results:
Log Likelihood = -1949.94851933536;
Shared Parameters:
kappa=0.290308

Tree constrained3TaxaTree=(Ingroup1:0.0116144,Ingroup2:0.0236941,OutGroup:0.229394);


-2(Ln Likelihood Difference)=0.108964
Difference in number of parameters:1
P-Value:0.741327


For constrained, I expect Ingroup1 == Ingroup2

Hi Darrell,

[code]
(Ingroup1:0.0116144,Ingroup2:0.0236941,OutGroup:0.229394)
[/code]

lists branch lengths (i.e. a weighted sum of syn and non-syn rates), and you are only constraining non-syn rates (i.e. syn rates can vary between the ingroups).

Sergei