
_Matrix
Base class for distance matrix or scoring matrix.


DistanceMatrix
Distance matrix class that can be used for distance based tree algorithms.


_DistanceMatrix
Distance matrix class that can be used for distance based tree algorithms.


DistanceCalculator
Class to calculate the distance matrix from a DNA or Protein.


TreeConstructor
Base class for all tree constructor.


DistanceTreeConstructor
Distance based tree constructor.


Scorer
Base class for all tree scoring methods.


TreeSearcher
Base class for all tree searching methods.


NNITreeSearcher
Tree searching with Nearest Neighbor Interchanges (NNI) algorithm.


ParsimonyScorer
Parsimony scorer with a scoring matrix.


ParsimonyTreeConstructor
Parsimony tree constructor.
