| 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 | 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 | Description |
|---|---|
| MolecularClockLikelihoodModel.Instance |
| Class | Description |
|---|---|
| SiteDetails |
| Class | 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.
|