Package | Description |
---|---|
pal.substmodel |
Classes describing substitution models, i.e.
|
Modifier and Type | Class | Description |
---|---|---|
class |
GeneralPoissonRateMatrix |
A general rate matrix class for JC69/F81 style rate matrices (but for all data types)
|
class |
GeneralREVRateMatrix |
A general rate matrix class for REV style rate matrices (GTR but for all data types)
Includes the ability for arbitarily constraints
|
Modifier and Type | Method | Description |
---|---|---|
static SubstitutionModel |
SubstitutionModel.Utils.createSubstitutionModel(NeoRateMatrix rm,
DataType dt,
double[] equilibriumFrequencies) |
Constructor | Description |
---|---|
GeneralRateDistributionSubstitutionModel(NeoRateMatrix base,
RateDistribution rateDistribution,
DataType dt,
double[] frequencies) |
|
MultiRateMatrixHandler(NeoRateMatrix[] rateMatrices,
double[] equilibriumFrequencies,
double[] initialClassProportions) |
|
RateMatrixHandler(NeoRateMatrix rateMatrix,
double[] equilibriumFrequencies) |
|
SimpleRateMatrixGroup(NeoRateMatrix[] baseMatrices,
double[] equilibriumFrequencies,
double[] initialClassProbabilities,
DataType dataType) |
|
SingleClassSubstitutionModel(NeoRateMatrix base,
DataType dt,
double[] frequencies) |