Package | Description |
---|---|
pal.eval |
Classes for evaluating evolutionary hypothesis (chi-square and likelihood
criteria) and estimating model parameters.
|
pal.mep |
Classes for the analysis of "measurably evolving populations" (mep).
|
pal.statistics |
Classes with useful for statistics (normal distribution,
Gamma distribution, chi-square distribution, exponential distribution,
likelihood-ratio test, chi-square test, descriptive statistics, bootstrap estimators etc.)
|
pal.treesearch |
Class and Description |
---|
ConditionalProbabilityStore
Title: ConditionalProbabilityStore (was ConditionalLikelihoodStore)
|
ConditionalProbabilityStore.ExtraProcessor |
LHCalculator |
LHCalculator.External
The External calculator does not maintain any state and is approapriate for
calculation where a store is provided
|
LHCalculator.Factory |
LHCalculator.Generator |
LHCalculator.Internal
The Internal calculator may maintain state and is approapriate permanent attachment
to internal nodes of the tree structure
|
LHCalculator.Leaf
A LHCalculator.Leaf object is attached to each leaf node and can be used to calculated conditional probabilities across the related branch.
|
LikelihoodCalculator
classes that calculate likelihoods should implement this interface.
|
LikelihoodSummary |
LikelihoodValue
Computes the likelihood for a tree given a
model of sequence evolution and a sequence alignment;
also optimises tree parameters such as branch lengths
by maximising the likelihood (for optimal performance
special optimisation procedures are
employed for UnconstrainedTree, ClockTree and DatedTipsClockTree;
a general optimisation precedure is used for another
ParameterizedTree).
|
MolecularClockLikelihoodModel |
MolecularClockLikelihoodModel.External
The External calculator does not maintain any state and is approapriate for
calculation where a store is provided
|
MolecularClockLikelihoodModel.HeightConverter |
MolecularClockLikelihoodModel.Instance |
MolecularClockLikelihoodModel.Internal
The Internal calculator may maintain state and is approapriate permanent attachment
to internal nodes of the tree structure
|
MolecularClockLikelihoodModel.Leaf
A ConstrainedLHCalculator.Leaf object is attached to each leaf node and can be used to calculated conditional probabilities across the related branch.
|
PatternInfo
Title: PatternInfo
|
SiteDetails |
UnconstrainedLikelihoodModel |
UnconstrainedLikelihoodModel.External
The External calculator does not maintain any state and is approapriate for
calculation where a store is provided
|
UnconstrainedLikelihoodModel.Instance |
UnconstrainedLikelihoodModel.Internal
The Internal calculator may maintain state and is approapriate permanent attachment
to internal nodes of the tree structure
|
UnconstrainedLikelihoodModel.Leaf
A LHCalculator.Leaf object is attached to each leaf node and can be used to calculated conditional probabilities across the related branch.
|
Class and Description |
---|
MolecularClockLikelihoodModel.Instance |
Class and Description |
---|
SiteDetails |
Class and Description |
---|
ConditionalProbabilityStore
Title: ConditionalProbabilityStore (was ConditionalLikelihoodStore)
|
LHCalculator.Factory |
MolecularClockLikelihoodModel.External
The External calculator does not maintain any state and is approapriate for
calculation where a store is provided
|
MolecularClockLikelihoodModel.HeightConverter |
MolecularClockLikelihoodModel.Instance |
MolecularClockLikelihoodModel.Internal
The Internal calculator may maintain state and is approapriate permanent attachment
to internal nodes of the tree structure
|
MolecularClockLikelihoodModel.Leaf
A ConstrainedLHCalculator.Leaf object is attached to each leaf node and can be used to calculated conditional probabilities across the related branch.
|
PatternInfo
Title: PatternInfo
|
SiteDetails |
UnconstrainedLikelihoodModel.External
The External calculator does not maintain any state and is approapriate for
calculation where a store is provided
|
UnconstrainedLikelihoodModel.Instance |
UnconstrainedLikelihoodModel.Internal
The Internal calculator may maintain state and is approapriate permanent attachment
to internal nodes of the tree structure
|
UnconstrainedLikelihoodModel.Leaf
A LHCalculator.Leaf object is attached to each leaf node and can be used to calculated conditional probabilities across the related branch.
|