Uses of Package
Likelihood

Packages that use Likelihood
Likelihood Provides classes for calculating the likelihood of a tree given a model and an alignment. 
Optimizers Provides classes for optimising a likelihood. 
 

Classes in Likelihood used by Likelihood
Calculator
          Calculates the likelihood for different parameter values.
Likelihood
          Stores the results of a likelihood calculation.
Likelihood.LikelihoodException
          Exception related to a likelihood calculation
Likelihood.NodeLikelihood
          Stores the results of a likelihood claculation for a single node in a tree.
Likelihood.RateLikelihood
          Stores the result of the likelihood calculations for a single site and a single rate class.
Likelihood.SiteLikelihood
          Stored the result of a likelihood calculation for a single site
Probabilities
          Stores the values of each transition, frequency etc for one set of parameters.
 

Classes in Likelihood used by Optimizers
Calculator
          Calculates the likelihood for different parameter values.
Likelihood
          Stores the results of a likelihood calculation.