Hi all,
In the constructor for GammaDiscreteRateDistribution objects, there is a mistake, imho: the value of 1.0 for alpha (shape parameter) is just a default one, and the user is allowed to specify a different one. But this is discarded on line 54 of file Bpp/Phyl/Model/RateDistribution/GammaDiscreteRateDistribution.h, where the current code calls the base class as:
GammaDiscreteDistribution(nbClasses, 1., 1.)
and it should be:
GammaDiscreteDistribution(nbClasses, alpha, alpha)
Cheers,
Jean-Baka