See: Description
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.
|
Exceptions |
Provides exceptions that are common across the package.
|
Executable |
Provides a general driver executable and an example executable
|
Likelihood |
Provides classes for calculating the likelihood of a tree given a model and
an alignment.
|
Maths |
Provides maths classes.
|
Models |
Provides classes for defing a phylogenetic model.
|
Optimizers |
Provides classes for optimising a likelihood.
|
Parameters |
Provides classes for defining parameters used in the various calculations.
|
Simulations |
Provides a class to create simulate data.
|
Trees |
Provides classes to define a tree and any constraints on that tree.
|
Utils |
Provides various utility classes.
|