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

Class Summary
AlignmentDistanceMatrix compute distance matrix (observed and ML) from alignment (SitePattern)
DistanceMatrix storage for pairwise distance matrices. features: - printing in in PHYLIP format, - computation of (weighted) squared distance to other distance matrix - Fills in all of array...
DistanceMatrixUtils Auxillary functions for distance matrices
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
SUPGMADistanceMatrix Corrects distances in a distance matrix such that all tips appear contemporaneous, given a time/date and rate information for the taxa.
 

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).