This software was compiled for 64bit Windows by Andre Falcao (afalcao at di.fc.ul.pt) 
from the source code provided by the Hisat2 authors available at:

https://ccb.jhu.edu/software/hisat2/index.shtml

Three important notes:
* The .exe files were compiled with cygwin. For the programs to run, the 3 Cygwin DLLs
  provided (cyggcc_s-seh-1.dll, cygstdc++-6.dll and cygwin1.dll) must be in the same 
  folder as the .exe files or directly accessible by Windows 
* The Python code from the original package is provided in a separate Python folder
  for file organization
* The hisat2 file is a PERL script and is the recommended way to run Hisat2 but it 
  requires a PERL interpreter (Strawberry PERL recommended)

Finally a disclaimer:
I GIVE NO WARRANTIES. I PROVIDE THE .EXE FILES IN THE HOPE THEY MIGHT BE USEFUL. 
THIS SOFTWARE IS PROVIDED "AS IS" WITH NO WARRANTIES WHATSOEVER.