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).