first commit, workable code
Basic definitions and operations
add BinaryCost
Add BinaryCost test.
add linear time gene tree refinement algorithm
renamed files
add util_simu and test
make refine and reconstruct in different functions.
4 gene tree refinement methods
bug fix of refinegt_weighted
use * to denote duplication node
minor bugfix
clean up
fix version
more test
add new method for affine cost
add new method
fix weight for affine method
clean up
add error check after refinement