Uses of Interface
pal.substmodel.NeoRateMatrix
Packages that use NeoRateMatrix
-
Uses of NeoRateMatrix in pal.substmodel
Classes in pal.substmodel that implement NeoRateMatrixModifier and TypeClassDescriptionclass
A general rate matrix class for JC69/F81 style rate matrices (but for all data types)class
A general rate matrix class for REV style rate matrices (GTR but for all data types) Includes the ability for arbitarily constraintsMethods in pal.substmodel with parameters of type NeoRateMatrixModifier and TypeMethodDescriptionstatic final SubstitutionModel
SubstitutionModel.Utils.createSubstitutionModel
(NeoRateMatrix rm, DataType dt, double[] equilibriumFrequencies) Constructors in pal.substmodel with parameters of type NeoRateMatrixModifierConstructorDescriptionGeneralRateDistributionSubstitutionModel
(NeoRateMatrix base, RateDistribution rateDistribution, DataType dt, double[] frequencies) MultiRateMatrixHandler
(NeoRateMatrix[] rateMatrices, double[] equilibriumFrequencies, double[] initialClassProportions) RateMatrixHandler
(NeoRateMatrix rateMatrix, double[] equilibriumFrequencies) SimpleRateMatrixGroup
(NeoRateMatrix[] baseMatrices, double[] equilibriumFrequencies, double[] initialClassProbabilities, DataType dataType) SingleClassSubstitutionModel
(NeoRateMatrix base, DataType dt, double[] frequencies)