| 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.
|