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)