Package Likelihood

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

See:
          Description

Class Summary
Calculator Calculates the likelihood for different parameter values.
Calculator.SiteCalculator Calculates the likelihood of a single site.
ConfidenceInterval Used to calculate congfidence intervals for a parameter.
Likelihood Stores the results of 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.
 

Exception Summary
Likelihood.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 clases for calculating the likelihood, storing the result, claculating confidence intervals.