Synonymous Sites Exporting

[Victor DeFilippis]

Dear Anyone:

I am looking for a program that can take my aligned (homologous) 
sequences and create export files (text, PHYLIP, MEGA, PAUP, etc.) of 
specific (or user specified) positions only.  For example, only 
synonymous positions, only nonsynonymous positions, only fourfold
degenerate sites, only twofold degenerate sites, etc.  I know that 
MEGA can make exports of only variable positions but can it do 
anything like I've described above?  Any assistance/information would 
be greatly appreciated.  Thanks in advance.

Victor DeFilippis
Wayne State University
vicdef at biology.biosci.wayne.edu