Package pal.distance
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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ClassDescriptioncompute distance matrix (observed and ML) from alignment (SitePattern)storage for pairwise distance matrices.Auxillary functions for distance matricesexception thrown by ReadDistanceMatrixcompute jukes-cantor corrected distance matrixdetermines the (observed and ML) distance between a pair of sequencesreads pairwise distance matrices in PHYLIP format (full matrix)computation of the (negative) log-likelihood for a pair of sequences