Package pal.distance
Classes for reading and generating distance matrices, including computation
of pairwise distances for sequence data (maximum-likelihood and observed
distances).
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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 matricesDistanceTool JukesCantorDistanceMatrix compute jukes-cantor corrected distance matrixPairwiseDistance determines the (observed and ML) distance between a pair of sequencesReadDistanceMatrix 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