Package org.biojava.nbio.phylo

Class Summary

Class	Description
Comparison	This class provides static methods for the calculation of the percentage of identity between two aligned sequences.
DistanceMatrixCalculator	The DistanceMatrixCalculator methods generate a DistanceMatrix from a MultipleSequenceAlignment or other indirect distance infomation (RMSD).
DistanceTreeEvaluator	Check the accuracy of a Distance Tree by least squares error (LSE) of the Tree branch lengths and the original Distance Matrix.
ForesterWrapper	This class contains wrapper methods for communication between BioJava and forester (e.g, Data Structure conversion).
TreeConstructor	The TreeConstructor uses the forester library to build different types of phylogenetic trees.

Enum Summary

Enum	Description
TreeConstructorType	The TreeConstructorType specifies the aligorithm used to construct the tree (clustering algorithm).
TreeType	The TreeType specifies the optimization criteria used to generate the tree.