Uses of Package
pal.eval

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.