Uses of Class
pal.substmodel.RateDistribution
Packages that use RateDistribution
Package
Description
Classes for evaluating evolutionary hypothesis (chi-square and likelihood
criteria) and estimating model parameters.
Classes describing substitution models, i.e.
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 RateDistributionModifierConstructorDescriptionGeneralLikelihoodCalculator
(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.substmodelModifier and TypeClassDescriptionclass
discrete Gamma distribution (Z.class
invariable sites model (two-rate model with mean rate = 1.0)class
uniform rate distributionMethods in pal.substmodel with parameters of type RateDistributionModifier and TypeMethodDescriptionstatic final SubstitutionModel
SubstitutionModel.Utils.createSubstitutionModel
(RateMatrix rm, RateDistribution rd) static final SubstitutionModel
SubstitutionModel.Utils.createSubstitutionModel
(RateMatrix rm, RateDistribution rd, boolean parameteriseDistribution) Constructors in pal.substmodel with parameters of type RateDistributionModifierConstructorDescriptionGeneralRateDistributionSubstitutionModel
(NeoRateMatrix base, RateDistribution rateDistribution, DataType dt, double[] frequencies) -
Uses of RateDistribution in pal.xml
Methods in pal.xml that return RateDistributionModifier and TypeMethodDescriptionstatic RateDistribution
ElementParser.parseRateDistribution
(Element e)