|
||||||||||
PREV NEXT | FRAMES NO FRAMES |
Packages that use pal.eval | |
---|---|
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 |
Classes in pal.eval used by pal.eval | |
---|---|
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. |
Classes in pal.eval used by pal.mep | |
---|---|
MolecularClockLikelihoodModel.Instance
|
Classes in pal.eval used by pal.statistics | |
---|---|
SiteDetails
|
Classes in pal.eval used by pal.treesearch | |
---|---|
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. |
|
||||||||||
PREV NEXT | FRAMES NO FRAMES |