Package | Description |
---|---|
pal.misc |
Classes that don't fit elsewhere ;^)
|
pal.substmodel |
Classes describing substitution models, i.e.
|
Modifier and Type | Class | Description |
---|---|---|
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)
|
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 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. |