Uses of Interface
pal.substmodel.NeoRateMatrix
-
Packages that use NeoRateMatrix Package Description pal.substmodel Classes describing substitution models, i.e. -
-
Uses of NeoRateMatrix in pal.substmodel
Classes in pal.substmodel that implement NeoRateMatrix Modifier and Type Class Description class
GeneralPoissonRateMatrix
A general rate matrix class for JC69/F81 style rate matrices (but for all data types)class
GeneralREVRateMatrix
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 NeoRateMatrix Modifier and Type Method Description static SubstitutionModel
SubstitutionModel.Utils. createSubstitutionModel(NeoRateMatrix rm, DataType dt, double[] equilibriumFrequencies)
Constructors in pal.substmodel with parameters of type NeoRateMatrix Constructor Description GeneralRateDistributionSubstitutionModel(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)
-