Uses of Package
Utils

Packages that use Utils
Alignments Provides class for dealing with "alignments" and the sites in an alignment. 
Likelihood Provides classes for calculating the likelihood of a tree given a model and an alignment. 
Models Provides classes for defing a phylogenetic model. 
Utils Provides various utility classes. 
 

Classes in Utils used by Alignments
ArrayMap
          A crude map of a fixed size that is backed by an array.
 

Classes in Utils used by Likelihood
ArrayMap
          A crude map of a fixed size that is backed by an array.
Range
          Used to represent a range (using doubkes)
 

Classes in Utils used by Models
ArrayMap
          A crude map of a fixed size that is backed by an array.
 

Classes in Utils used by Utils
PossibleSettings
          Maintains a list of possible settings.
SetSettings
          Represents the value of settings.
SettingException
          Exception thrown when there is a problem with the Settings machinery
SetUtils.SetHasMultipleElementsException
          Exception thrown if an attempt is made to get the single element from a set that has multiple elements.