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.
|