Package pal.distance

Classes for reading and generating distance matrices, including computation of pairwise distances for sequence data (maximum-likelihood and observed distances).

See:
          Description

Interface Summary
DistanceMatrixAccess  
DistanceMatrixGenerator  
 

Class Summary
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
DistanceParseException exception thrown by ReadDistanceMatrix
 

Package pal.distance Description

Classes for reading and generating distance matrices, including computation of pairwise distances for sequence data (maximum-likelihood and observed distances).