First upload: version e8a554 from sourceforge

Align.cpp

Align.hpp

Definitions.hpp

Energy.cpp

Energy.hpp

Options.cpp

Options.hpp

Sequence.cpp

Sequence.hpp

Util.cpp

Util.hpp

format_r_seq.sh

kseq.h

parameters/dangle.txt

parameters/dangle_text.txt

parameters/int11.txt

parameters/int21.txt

parameters/int22.txt

parameters/stack.txt

parameters/tstack.txt