Uses of Package
Alignments

Packages that use Alignments

Package	Description
Alignments	Provides class for dealing with "alignments" and the sites in an alignment.
Ancestors	Provides classed to calculate ancestral reconstruction.
Likelihood	Provides classes for calculating the likelihood of a tree given a model and an alignment.
ModelTest
Simulations	Provides a class to create simulated data.

Classes in Alignments used by Alignments

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

Classes in Alignments used by Ancestors

Class and Description
Alignment Represents an "alignment", used very loosely.
AlignmentException Exception related to an alignment (currently only input errors)
Site Represents a "site" in an "alignment".

Classes in Alignments used by Likelihood

Class and Description
Alignment Represents an "alignment", used very loosely.
AlignmentException Exception related to an alignment (currently only input errors)
Site Represents a "site" in an "alignment".

Classes in Alignments used by ModelTest

Class and Description
Alignment Represents an "alignment", used very loosely.

Classes in Alignments used by Simulations

Class and Description
Alignment Represents an "alignment", used very loosely.
AlignmentException Exception related to an alignment (currently only input errors)
Site Represents a "site" in an "alignment".