Uses of Package
Models

Packages that use Models
Ancestors Provides classed to calculate ancestral reconstruction. 
Likelihood Provides classes for calculating the likelihood of a tree given a model and an alignment. 
Models Provides classes for defing a phylogenetic model. 
Optimizers Provides classes for optimising a likelihood. 
Simulations Provides a class to create simulate data. 
 

Classes in Models used by Ancestors
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
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 Models
Distributions.Calculation
          Enumeration of the different methods of calculating a distribution
Distributions.DistributionsException
          Exception for use there is a problem calculating a distribution
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 Optimizers
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 Simulations
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