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