Package | Description |
---|---|
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.
|
Class and Description |
---|
Alignment
Represents an "alignment", used very losely.
|
AlignmentException
Exception related to an alignment (currently only input errors)
|
Ambiguous
Stores details of ambiguous characters
|
Site
Represents a "site" in an "alignment".
|
Class and Description |
---|
Alignment
Represents an "alignment", used very losely.
|
AlignmentException
Exception related to an alignment (currently only input errors)
|
Site
Represents a "site" in an "alignment".
|
Class and Description |
---|
Site
Represents a "site" in an "alignment".
|
Class and Description |
---|
Alignment
Represents an "alignment", used very losely.
|
Site
Represents a "site" in an "alignment".
|
Class and Description |
---|
Alignment
Represents an "alignment", used very losely.
|
AlignmentException
Exception related to an alignment (currently only input errors)
|
Site
Represents a "site" in an "alignment".
|