Uses of Class
pal.substmodel.GeneralREVRateMatrix

Packages that use GeneralREVRateMatrix
pal.substmodel Classes describing substitution models, i.e. 
 

Uses of GeneralREVRateMatrix in pal.substmodel
 

Methods in pal.substmodel that return GeneralREVRateMatrix
static GeneralREVRateMatrix GeneralREVRateMatrix.createGTR()
          Create a rate matrix equivalent to the GTR model
static GeneralREVRateMatrix GeneralREVRateMatrix.createGTR(double[] defaultParameters)
          Create a rate matrix equivalent to the GTR model
static GeneralREVRateMatrix GeneralREVRateMatrix.createGTR(double a, double b, double c, double d, double e)
          Create a rate matrix equivalent to the GTR model Parameters laid out * -> + A C G T A * a b c C * * d e G * * * 1 T * * * *
static GeneralREVRateMatrix GeneralREVRateMatrix.createHKY()
          Create a rate matrix equivalent to the HKY model, the one parameter will be kappa
static GeneralREVRateMatrix GeneralREVRateMatrix.createHKY(double defaultKappa)
          Create a rate matrix equivalent to the HKY model, the one parameter will be kappa