Uses of Package
Likelihood

Packages that use Likelihood

Package	Description
Alignments	Provides class for dealing with "alignments" and the sites in an alignment.
Ancestors	Provides classed to calculate ancestral reconstruction.
Likelihood	Provides classes for calculating the likelihood of a tree given a model and an alignment.
ModelTest
Models	Provides classes for defining a phylogenetic model.
Optimizers	Provides classes for optimising a likelihood.

Classes in Likelihood used by Alignments

Class and Description
SiteLikelihood.LikelihoodException Exception related to a likelihood calculation
SiteLikelihood.NodeLikelihood Stores the results of a likelihood calculation for a single node in a tree.

Classes in Likelihood used by Ancestors

Class and Description
SiteLikelihood.LikelihoodException Exception related to a likelihood calculation
SiteLikelihood.NodeLikelihood Stores the results of a likelihood calculation for a single node in a tree.

Classes in Likelihood used by Likelihood

Class and Description
Calculator Abstract class for calculating a likelihood.
Calculator.CalculatorException Exception thrown when there is a problem with the calculation
Likelihood Represents the simplest possible likelihood result, i.e.
Probabilities Stores the values of each transition, frequency etc for one set of parameters.
Probabilities.RateProbabilities Stores the values of each transition, frequency etc for one set of parameters and for a single rate category.
Root Provides information on what to do once the root of the tree is reached.
SiteLikelihood Stored the result of a likelihood calculation for a single site
SiteLikelihood.LikelihoodException Exception related to a likelihood calculation
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.

Classes in Likelihood used by ModelTest

Class and Description
Calculator Abstract class for calculating a likelihood.
Likelihood Represents the simplest possible likelihood result, i.e.

Classes in Likelihood used by Models

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

Classes in Likelihood used by Optimizers

Class and Description
Likelihood Represents the simplest possible likelihood result, i.e.