Uses of Interface
pal.substmodel.NeoRateMatrix

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

Uses of NeoRateMatrix in pal.substmodel
 

Classes in pal.substmodel that implement NeoRateMatrix
 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 constraints
 

Methods in pal.substmodel with parameters of type NeoRateMatrix
static SubstitutionModel SubstitutionModel.Utils.createSubstitutionModel(NeoRateMatrix rm, DataType dt, double[] equilibriumFrequencies)
           
 

Constructors in pal.substmodel with parameters of type NeoRateMatrix
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)