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See:
Description
Interface Summary | |
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DistanceMatrixAccess | |
DistanceMatrixGenerator |
Class Summary | |
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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 | |
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DistanceParseException | exception thrown by ReadDistanceMatrix |
Classes for reading and generating distance matrices, including computation of pairwise distances for sequence data (maximum-likelihood and observed distances).
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