Package pal.eval

Classes for evaluating evolutionary hypothesis (chi-square and likelihood criteria) and estimating model parameters.

See:
          Description

Interface Summary
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.
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.
MolecularClockLikelihoodModel.Simulator  
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 Summary
ChiSquareValue computes chi-square value of a (parameterized) tree for its set of parameters (e.g., branch lengths) and a given distance matrix
ConditionalProbabilityStore Title: ConditionalProbabilityStore (was ConditionalLikelihoodStore)
DemographicLikelihoodValue Estimates the likelihood for a tree using a specified model of sequence evolution and a sequence alignment and a specific demographic model as a prior on coalescent intervals.
DemographicValue estimates demographic parameters by maximising the coalescent prior for a tree with given branch lengths.
FastFourStateLHCalculator  
FastLikelihoodCalculator Title: Fast Likelihood Calculator
Description: A fast likelihood calculator
Original code by Matthew Goode.
GeneralLikelihoodCalculator Title: General Likelihood Calculator
Description: A General likelihood calculator
This calculates the likelihood of an topologically invariant tree (on an unchanging alignment) quickly by remembering partial likelihoods of invariant subtrees, and by essentially generating site patterns for each sub tree.
LHCalculator.AbstractExternal  
LikelihoodOptimiser  
LikelihoodSummary  
LikelihoodTool  
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).
ModelParameters estimates substitution model parameters from the data
PatternInfo Title: PatternInfo
SimpleLeafCalculator  
SimpleLHCalculator  
SimpleLikelihoodCalculator  
SimpleModelFastFourStateLHCalculator  
SimpleMolecularClockLikelihoodModel  
SimpleUnconstrainedLikelihoodModel  
SimpleUnconstrainedLikelihoodModel.InternalImpl  
SimpleUnconstrainedLikelihoodModel.LeafImpl  
SingleSplitMolecularClockLikelihoodModel  
SiteDetails.Utils  
 

Package pal.eval Description

Classes for evaluating evolutionary hypothesis (chi-square and likelihood criteria) and estimating model parameters.