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