+ options - checked that output is unchanged by running on final*.{msa,nw} and passing to md5sum
def out fname option implemented.
output filename option ok
adding Pep model by forking Nuc model
PepModel.hs compiles
Align now compiles with CladeModel as data
CladeModel now instance of Binary
Output.hs compiles
mlgsc (and deps thereof) compiles
All binaries compile and run w/o apparent probs (no diff WRT before refactoring). Tests will need a major rewrite, and protein still not fully implemented