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In their 1994 paper "Volume Changes in Protein Evolution",
Gerstein, Sonnhammer and Chothia developed a weighting
procedure for protein sequences to avoid over-represented
sequences in the appendix "A Method to Weight Protein
Sequences to Correct for Unequal Representation". Although
their method was developed for protein sequences, it is readily
extended to work on any measurable set.
This package calculates GSC weights for any reasonable
dendrogram. If you want to recreate their algorithm, then just
use UPGMA as linkage and residue identity as distance
function when creating the dendrogram.
Changes in version 0.2:
Updated to work with hierarchical-clustering 0.4.
Changes in version 0.1.1.1:
Use an stricter upper bound on hierachical-clustering.
Changes in version 0.1.1:
Now works even when some (or all) branches have distance zero
(i.e. elements below that branches are all equal with respect
to distance metric that was used to create the dendrogram).
