Package Likelihood

Provides classes for calculating the likelihood of a tree given a model and an alignment.

See: Description

Interface Summary

Interface	Description
Root	Provides information on what to do once the root of the tree is reached.

Class Summary

Class	Description
Calculator<R extends Likelihood>	Abstract class for calculating a likelihood.
ConfidenceInterval	Used to calculate confidence intervals for a parameter.
FitzJohnRoot	Root class for the FitzJohn et al 2009 method
Likelihood	Represents the simplest possible likelihood result, i.e.
Probabilities	Stores the values of each transition, frequency etc for one set of parameters.
SiteLikelihood	Stored the result of a likelihood calculation for a single site
SiteLikelihood.NodeLikelihood	Stores the results of a likelihood calculation for a single node in a tree.
SiteLikelihood.RateLikelihood	Stores the result of the likelihood calculations for a single site and a single rate class.
StandardCalculator	Calculates the likelihood for different parameter values.
StandardLikelihood	Stores the results of a likelihood calculation.
StandardRoot	Root class for the standard root methods - e.g.

Exception Summary

Exception	Description
Calculator.CalculatorException	Exception thrown when there is a problem with the calculation
SiteLikelihood.LikelihoodException	Exception related to a likelihood calculation

Package Likelihood Description

Provides classes for calculating the likelihood of a tree given a model and an alignment. There are classes for calculating the likelihood, storing the result, calculating confidence intervals.