This library provides classes to perform likelihood calculations on phylogenetic trees.

See: Description

Packages 
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.