Uses of Package
Models

Packages that use Models

Package	Description
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.
Simulations	Provides a class to create simulated data.

Classes in Models used by Ancestors

Class and Description
Model Represents an evolutionary model.
Model.ModelException Exception thrown when there is a problem with the model
RateCategory.RateException Exception thrown if there is a problem within a RateClass

Classes in Models used by Likelihood

Class and Description
Model Represents an evolutionary model.
Model.ModelException Exception thrown when there is a problem with the model
RateCategory Represents a rate category of a phylogenetic model.
RateCategory.RateException Exception thrown if there is a problem within a RateClass

Classes in Models used by ModelTest

Class and Description
Model Represents an evolutionary model.

Classes in Models used by Models

Class and Description
Distributions.Calculation Enumeration of the different methods of calculating a distribution
Distributions.DistributionsException Exception for use there is a problem calculating a distribution
DNAModelFactory.DNAModel Represents the various types of DNA models
Model Represents an evolutionary model.
Model.ModelException Exception thrown when there is a problem with the model
RateCategory Represents a rate category of a phylogenetic model.
RateCategory.FrequencyType Enumeration of the different ways of defining the root frequency
RateCategory.RateException Exception thrown if there is a problem within a RateClass

Classes in Models used by Simulations

Class and Description
Model Represents an evolutionary model.
Model.ModelException Exception thrown when there is a problem with the model
RateCategory.RateException Exception thrown if there is a problem within a RateClass