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See:
Description
Interface Summary | |
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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 | |
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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 |
Classes for evaluating evolutionary hypothesis (chi-square and likelihood criteria) and estimating model parameters.
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