Uses of Class
pal.substmodel.RateDistribution

Packages that use RateDistribution
pal.eval Classes for evaluating evolutionary hypothesis (chi-square and likelihood criteria) and estimating model parameters. 
pal.substmodel Classes describing substitution models, i.e. 
pal.xml Utility classes for converting PAL objects to and from XML documents. 
 

Uses of RateDistribution in pal.eval
 

Constructors in pal.eval with parameters of type RateDistribution
GeneralLikelihoodCalculator(Alignment baseAlignment, Tree tree, RateMatrix model, RateDistribution distribution)
          Constructor taking site pattern, tree rate matrix, and a rate distribution
 

Uses of RateDistribution in pal.substmodel
 

Subclasses of RateDistribution in pal.substmodel
 class GammaRates
          discrete Gamma distribution (Z.
 class InvariableSites
          invariable sites model (two-rate model with mean rate = 1.0)
 class UniformRate
          uniform rate distribution
 

Methods in pal.substmodel with parameters of type RateDistribution
static SubstitutionModel SubstitutionModel.Utils.createSubstitutionModel(RateMatrix rm, RateDistribution rd)
           
static SubstitutionModel SubstitutionModel.Utils.createSubstitutionModel(RateMatrix rm, RateDistribution rd, boolean parameteriseDistribution)
           
 

Constructors in pal.substmodel with parameters of type RateDistribution
GeneralRateDistributionSubstitutionModel(NeoRateMatrix base, RateDistribution rateDistribution, DataType dt, double[] frequencies)
           
 

Uses of RateDistribution in pal.xml
 

Methods in pal.xml that return RateDistribution
static RateDistribution ElementParser.parseRateDistribution(org.w3c.dom.Element e)