Uses of Class
pal.misc.PalObjectListener.EventGenerator
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Packages that use PalObjectListener.EventGenerator Package Description pal.misc Classes that don't fit elsewhere ;^)pal.substmodel Classes describing substitution models, i.e. -
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Uses of PalObjectListener.EventGenerator in pal.misc
Subclasses of PalObjectListener.EventGenerator in pal.misc Modifier and Type Class Description static class
Parameterized.ParameterizedBase
A Utility class for using as the superclass to subclasses which are based on double arraysstatic 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 Modifier and Type Class Description 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 distributionclass
SingleClassSubstitutionModel
class
UniformRate
uniform rate distributionstatic 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.
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