Uses of Class
Likelihood.Probabilities

Packages that use Probabilities

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

Uses of Probabilities in Likelihood

Methods in Likelihood with parameters of type Probabilities

Modifier and Type	Method and Description
abstract SiteLikelihood	Calculator.calculateSite(Site s, Tree t, Parameters p, Probabilities tp, java.util.Map<java.lang.String,SiteLikelihood.NodeLikelihood> nl) Calculate the likelihood for a single site.
SiteLikelihood	StandardCalculator.calculateSite(Site s, Tree t, Parameters p, Probabilities tp, java.util.Map<java.lang.String,SiteLikelihood.NodeLikelihood> nl)

Constructors in Likelihood with parameters of type Probabilities

Constructor and Description
Calculator.SiteCalculator(Site s, Tree t, Parameters p, Probabilities tp, java.util.Map<java.lang.String,SiteLikelihood.NodeLikelihood> nl) Standard constructor
SiteLikelihood(java.util.Map<RateCategory,SiteLikelihood.RateLikelihood> rateLikelihoods, Probabilities P) Default constructor