Uses of Class
pal.misc.PalObjectListener.EventGenerator

Packages that use PalObjectListener.EventGenerator
pal.misc Classes that don't fit elsewhere ;^) 
pal.substmodel Classes describing substitution models, i.e. 
 

Uses of PalObjectListener.EventGenerator in pal.misc
 

Subclasses of PalObjectListener.EventGenerator in pal.misc
static class Parameterized.ParameterizedBase
          A Utility class for using as the superclass to subclasses which are based on double arrays
static class Parameterized.ParameterizedUser
          A Utility class for using as the superclass to subclasses which work by adding functionality to a general Parameterized object (the base Parameterized object)
 

Uses of PalObjectListener.EventGenerator in pal.substmodel
 

Subclasses of PalObjectListener.EventGenerator in pal.substmodel
 class GammaRates
          discrete Gamma distribution (Z.
 class GeneralRateDistributionSubstitutionModel
           
 class InvariableSites
          invariable sites model (two-rate model with mean rate = 1.0)
 class RateDistribution
          abstract base class for models of rate variation over sites employing a discrete rate distribution
 class SingleClassSubstitutionModel
           
 class UniformRate
          uniform rate distribution
static class YangCodonModel.SimpleNeutralSelection
          A Substitution Model which can be used to implment the Neutral Model (with out continuous rate stuff) Codon model of [1] which uses the weighted sum of trwo base YangCodon models where omega=0, omega=1 repectively
[1] Nielsen, R., Yang Z., 1998 Likelihood Models for Detecting Positively Selected Amino Acid Sites and Applications to the HIV-1 Envelope Gene.
static class YangCodonModel.SimplePositiveSelection
          A Substitution Model which can be used to implment the Postitive Selection (with out continuous rate stuff) Codon model of [1] which uses the weighted sum of a three base Codon model where omega=0, omega=1 and omega=free
[1] Nielsen, R., Yang Z., 1998 Likelihood Models for Detecting Positively Selected Amino Acid Sites and Applications to the HIV-1 Envelope Gene.