This directory and subdirectory contains utilities for analyzing 4d sites.  

In the "4d" subdirectory there is a tool called amalgam.pl which
amalgamets a lits of 4d sites into a single list. 

In this directory analyze analyzes the substitution activity at the 4d sites.
The analyze tool takes a raw "zoo" alignment, in which the first sequence is
human, and also in which the alignment coordinates correspond to the 
coordinates in the 4d list.  It then prints out a list of summary statistics.
