Uses of Package
Alignments

Packages that use Alignments
Alignments Provides class for dealing with "alignments" and the sites in an alignment. 
Ancestors Provides classed to calculate ancestral reconstruction. 
Constraints Provides classes to constrain the state of internal nodes. 
Likelihood Provides classes for calculating the likelihood of a tree given a model and an alignment. 
Simulations Provides a class to create simulate data. 
 

Classes in Alignments used by Alignments
Alignment
          Represents an "alignment", used very losely.
Alignment.UniqueSite
          Used to represent a unique site in an alignment.
AlignmentException
          Exception related to an alignment (currently only input errors)
Ambiguous
          Stores details of ambiguous characters
Site
          Represents a "site" in an "alignment".
 

Classes in Alignments used by Ancestors
Alignment
          Represents an "alignment", used very losely.
AlignmentException
          Exception related to an alignment (currently only input errors)
Site
          Represents a "site" in an "alignment".
 

Classes in Alignments used by Constraints
Site
          Represents a "site" in an "alignment".
 

Classes in Alignments used by Likelihood
Alignment
          Represents an "alignment", used very losely.
AlignmentException
          Exception related to an alignment (currently only input errors)
Site
          Represents a "site" in an "alignment".
 

Classes in Alignments used by Simulations
Alignment
          Represents an "alignment", used very losely.
AlignmentException
          Exception related to an alignment (currently only input errors)
Site
          Represents a "site" in an "alignment".