An R implementation of the Gerstein-Sonnhammer-Chothia algorithm described in:
Gerstein M, Sonnhammer ELL, Chothian C (1994) Volume Changes in Protein Evolution. Journal of Molecular Biology. doi:10.1016/0022-2836(94)90012-4
The algorithm is described in the paper's appendix titled, "A Method to Weight Protein Sequences to Correct for Unequal Representation." [Download PDF].
The algorithm weights the leaves of a dendrogram based on their underrepresentation.
Run the algorithm with the GSC() function from the GSC.R file. The single input to GSC() is a dendrogram object.