Package pal.distance

• Interface Summary 

  Interface	Description
  DistanceMatrixAccess
  DistanceMatrixGenerator

• Class Summary 

  Class	Description
  AlignmentDistanceMatrix	compute distance matrix (observed and ML) from alignment (SitePattern)
  DistanceMatrix	storage for pairwise distance matrices.
  DistanceMatrixAccess.Utils
  DistanceMatrixGenerator.Utils
  DistanceMatrixUtils	Auxillary functions for distance matrices
  DistanceTool
  JukesCantorDistanceMatrix	compute jukes-cantor corrected distance matrix
  PairwiseDistance	determines the (observed and ML) distance between a pair of sequences
  ReadDistanceMatrix	reads pairwise distance matrices in PHYLIP format (full matrix)
  SequencePairLikelihood	computation of the (negative) log-likelihood for a pair of sequences

• Exception Summary 

  Exception	Description
  DistanceParseException	exception thrown by ReadDistanceMatrix

Package pal.distance Description