make setup.py back
biopython tutorial using sphinx

update header
add __init__.py
add codon alphabet (inherited from Bio.Alphabet.Alphabet) for CodonSeq
implement simple codon alignment without mismatch and frameshift
small revisions
add index seq file support and test_data
change __getitem__ method of CodonSeq to incorporate the step slice
add CodonSeq object for codon slice
add mismatch support
add __str__ method to CodonAlignment for nice output
modify _str_line method in Generic.py for the ease of CodonAlignment __str__ method
modify unittest for CodonAlignment
delete _str_line method
replace self-defined exceptions with build-in exceptions
add toSeq method for CodonSeq (helpful to write it out)
add toMultipleSeqAlignment method for CodonAlignment
fix a bug of terminal anchor checking
add code for CodonAlignment -- MultipleSeqAlignment convertion
small bug (add a colon)