Package | Description |
---|---|
pal.coalescent |
Classes to model population genetic processes using the coalescent.
|
pal.eval |
Classes for evaluating evolutionary hypothesis (chi-square and likelihood
criteria) and estimating model parameters.
|
pal.gui |
GUI components for some special objects (e.g., trees).
|
pal.mep |
Classes for the analysis of "measurably evolving populations" (mep).
|
pal.misc |
Classes that don't fit elsewhere ;^)
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pal.substmodel |
Classes describing substitution models, i.e.
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pal.supgma | |
pal.tree |
Classes for providing the data structure of
trees, for constructing and modifying trees, and for parameterizing
trees (e.g., clock constraint).
|
pal.xml |
Utility classes for converting PAL objects to and from XML documents.
|
Modifier and Type | Method and Description |
---|---|
CoalescentIntervals |
SerialCoalescentSimulator.simulateIntervals(TimeOrderCharacterData tocd,
DemographicModel model,
boolean createTree)
Simulates a set of CoalescentIntervals from a genealogy.
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Constructor and Description |
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SerialCoalescentGenerator(TimeOrderCharacterData tocd,
DemographicModel demographicModel,
int numberOfTreesToGenerate)
Results will not contain alignments
|
SerialCoalescentGenerator(TimeOrderCharacterData tocd,
DemographicModel demographicModel,
int numberOfTreesToGenerate,
TreeOperation treeFinisher)
Results will not contain alignments
|
SerialCoalescentGenerator(TimeOrderCharacterData tocd,
DemographicModel demographicModel,
int numberOfTreesToGenerate,
TreeOperation treeFinisher,
SimulatedAlignment.Factory alignmentFactory) |
SerialCoalescentGenerator(TimeOrderCharacterData tocd,
DemographicModel demographicModel,
TreeOperation treeFinisher,
SimulatedAlignment.Factory alignmentFactory) |
Modifier and Type | Method and Description |
---|---|
static Tree |
LikelihoodTool.optimiseMRDT(Tree tree,
Alignment alignment,
SubstitutionModel model,
TimeOrderCharacterData tocd,
boolean optimiseModel,
double[] rateStore)
Optimise the branches of a tree with regard to maximum likelihood, with under an assumption of a molecular clock with serially sampled data and multiple mutation rate parameters, mu - one for each sampling interval.
|
static Tree |
LikelihoodTool.optimiseMRDT(Tree tree,
Alignment alignment,
SubstitutionModel model,
TimeOrderCharacterData tocd,
boolean optimiseModel,
double[] rateChangeTimes,
double[] rateStore)
Optimise the branches of a tree with regard to maximum likelihood, with under an assumption of a molecular clock with serially sampled data and multiple mutation rate parameters, mu, over general time intervals.
|
static Tree |
LikelihoodTool.optimiseSRDT(Tree tree,
Alignment alignment,
SubstitutionModel model,
TimeOrderCharacterData tocd,
boolean optimiseModel,
double[] rateStore)
Optimise the branches of a tree with regard to maximum likelihood, with under an assumption of a molecular clock with serially sampled data and a single mutation rate parameter.
|
Modifier and Type | Method and Description |
---|---|
TimeOrderCharacterData |
TreePainter.getTimeOrderCharacterData() |
Modifier and Type | Method and Description |
---|---|
void |
TreePainter.setTimeOrderCharacterData(TimeOrderCharacterData tocd) |
Constructor and Description |
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TreeComponent(Tree tree,
TimeOrderCharacterData tocd,
boolean usingSymbols) |
Modifier and Type | Method and Description |
---|---|
TimeOrderCharacterData |
MutationRateModel.scale(TimeOrderCharacterData toScale) |
Modifier and Type | Method and Description |
---|---|
DeltaModel.Instance |
DeltaModel.generateInstance(TimeOrderCharacterData tocd) |
static DeltaModel |
DeltaModel.Utils.getDisjointBased(DeltaModel primaryModel,
DeltaModel subgroupModel,
TimeOrderCharacterData subgroupTOCD) |
static MutationRateModel.Factory |
SteppedMutationRate.getFactory(double[] muChanges,
TimeOrderCharacterData tocd)
Generate a MutationRateModel.Factory class for a SteppedMutationRate
|
TimeOrderCharacterData |
MutationRateModel.scale(TimeOrderCharacterData toScale) |
Constructor and Description |
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SteppedMutationRate(double[] rates,
TimeOrderCharacterData timeInfo)
Construct mutation rate model of a give rate in given units.
|
SteppedMutationRate(double[] rates,
TimeOrderCharacterData timeInfo,
boolean fixed)
Construct mutation rate model of a give rate in given units.
|
Modifier and Type | Method and Description |
---|---|
static TimeOrderCharacterData |
TimeOrderCharacterData.clone(TimeOrderCharacterData tocd)
Returns a clone of the specified TimeOrderCharacterData
|
TimeOrderCharacterData |
TimeOrderCharacterData.createSubgroup(int subgroupNumber)
Creates a TimeOrderCharacterData which is a subset of this sub group.
|
TimeOrderCharacterData |
TimeOrderCharacterData.generateDummyTimedTOCD(double[] sampleRates) |
TimeOrderCharacterData |
TimeOrderCharacterData.generateExpectedSubsitutionsTimedTOCD(double[] sampleRates)
Given an array of rates between samples (matching exactly the samples in order) then
produces a TimeOrderCharacterData object that is timed by Expected Substitutions.
|
TimeOrderCharacterData |
TimeOrderCharacterData.getReordered(IdGroup base)
Creates a new TimeOrderCharacterData object with the same properites as this one
but the identifier positions match that of base (ie whichIdNumber(Name) returns the same as for base)
|
TimeOrderCharacterData |
TimeOrderCharacterData.scale(double rate,
int newUnits) |
TimeOrderCharacterData |
TimeOrderCharacterData.subset(IdGroup staxa)
Extracts a subset of a TimeOrderCharacterData.
|
Modifier and Type | Method and Description |
---|---|
static TimeOrderCharacterData |
TimeOrderCharacterData.clone(TimeOrderCharacterData tocd)
Returns a clone of the specified TimeOrderCharacterData
|
void |
TimeOrderCharacterData.setOrdinals(TimeOrderCharacterData tocd)
Set time ordinals from another TimeOrderCharacterData.
|
void |
TimeOrderCharacterData.setOrdinals(TimeOrderCharacterData tocd,
IdGroup standard,
boolean doTimes)
Set time ordinals from another TimeOrderCharacterData.
|
void |
TimeOrderCharacterData.setTimesAndOrdinals(TimeOrderCharacterData tocd) |
Constructor and Description |
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TOCDSampleInformation(TimeOrderCharacterData base) |
Modifier and Type | Method and Description |
---|---|
static TemporalModelChange |
TemporalModelChange.Utils.getSpecificTime(double time,
TimeOrderCharacterData tocd) |
Modifier and Type | Method and Description |
---|---|
void |
RateHandler.adjustDistances(double[][] matrix,
TimeOrderCharacterData tocd) |
void |
ThetaHandler.adjustDistances(double[][] matrix,
TimeOrderCharacterData tocd) |
DemographicModel |
ThetaHandler.generateDemographicModel(double[] deltas,
double[] thetas,
TimeOrderCharacterData tocd)
May return null if not possible to infer demographic model
|
MutationRateModel.Factory |
RateHandler.generateRateModelFactory(double[] deltas,
TimeOrderCharacterData tocd) |
int |
RateHandler.getNumberOfParameters(TimeOrderCharacterData tocd) |
int |
ThetaHandler.getNumberOfParameters(TimeOrderCharacterData tocd) |
Constructor and Description |
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SUPGMABase(DistanceMatrixAccess distanceAccess,
DistanceMatrixGenerator replicateGenerator,
TimeOrderCharacterData tocd) |
SUPGMADistanceMatrix(DistanceMatrix raw,
TimeOrderCharacterData tocd,
DeltaModel deltaModel)
Uses date/time information and a constant rate to correct distance matrices.
|
SUPGMATree(DistanceMatrix m,
TimeOrderCharacterData tocd,
DeltaModel deltaModel,
boolean allowNegatives,
ClusterTree.ClusteringMethod cm)
constructor SUPGMA tree
|
SUPGMATree(DistanceMatrix m,
TimeOrderCharacterData tocd,
double rate,
ClusterTree.ClusteringMethod cm)
constructor SUPGMA tree
|
Modifier and Type | Method and Description |
---|---|
static TimeOrderCharacterData |
TreeUtils.extractTimeOrderCharacterData(Tree tree,
int units)
Extracts a time order character data from a tree.
|
Modifier and Type | Method and Description |
---|---|
static ParameterizedTree.Factory |
MutationRateModelTree.getParameterizedTreeFactory(MutationRateModel.Factory rateModel,
TimeOrderCharacterData tocd)
Obtain a ParameterizedTree.Factory for generating Unconstrained trees
|
Constructor and Description |
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MutationRateModelTree(Tree t,
TimeOrderCharacterData tocd,
MutationRateModel model)
take any tree and afford it with an interface
suitable for a clock-like tree (parameters
are the minimal node height differences at each internal node).
|
MutationRateModelTree(Tree t,
TimeOrderCharacterData tocd,
MutationRateModel model,
boolean includeModelParameters)
take any tree and afford it with an interface
suitable for a clock-like tree (parameters
are the minimal node height differences at each internal node).
|
Modifier and Type | Method and Description |
---|---|
static TimeOrderCharacterData |
ElementParser.parseTimeDataElement(org.w3c.dom.Element e) |
Modifier and Type | Method and Description |
---|---|
static org.w3c.dom.Element |
ElementFactory.createTimeDataElement(TimeOrderCharacterData tocd,
org.w3c.dom.Document document) |