Uses of Interface
Likelihood.Root

Packages that use Root

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

Uses of Root in Likelihood

Classes in Likelihood that implement Root

Modifier and Type	Class and Description
class	FitzJohnRoot Root class for the FitzJohn et al 2009 method
class	StandardRoot Root class for the standard root methods - e.g.

Methods in Likelihood that return Root

Modifier and Type	Method and Description
Root	Probabilities.getRoot(RateCategory r) Get a root object, for the given rate category, that can be used to the total likelihood from the root node likelihoods or provide the frequencies of the various states at the root

Uses of Root in Models

Methods in Models that return Root

Modifier and Type	Method and Description
Root	RateCategory.getRoot() Get a root object that can be used to calculate the total likelihood from the root node likelihoods or provide the frequencies of the various states at the root