| Package | Description |
|---|---|
| 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.
|
| Constructor | Description |
|---|---|
GeneralLikelihoodCalculator(Alignment baseAlignment,
Tree tree,
RateMatrix model,
RateDistribution distribution) |
Constructor taking site pattern, tree rate matrix, and a rate distribution
|
| Modifier and Type | Class | Description |
|---|---|---|
class |
GammaRates |
discrete Gamma distribution (Z.
|
class |
InvariableSites |
invariable sites model (two-rate model with mean rate = 1.0)
|
class |
UniformRate |
uniform rate distribution
|
| Modifier and Type | Method | Description |
|---|---|---|
static SubstitutionModel |
SubstitutionModel.Utils.createSubstitutionModel(RateMatrix rm,
RateDistribution rd) |
|
static SubstitutionModel |
SubstitutionModel.Utils.createSubstitutionModel(RateMatrix rm,
RateDistribution rd,
boolean parameteriseDistribution) |
| Constructor | Description |
|---|---|
GeneralRateDistributionSubstitutionModel(NeoRateMatrix base,
RateDistribution rateDistribution,
DataType dt,
double[] frequencies) |
| Modifier and Type | Method | Description |
|---|---|---|
static RateDistribution |
ElementParser.parseRateDistribution(org.w3c.dom.Element e) |