After downloading a program, you can run it as follows:
         program_name   treeFile_1   treeFile_2   OPTION
where OPTION is a string in the set {HN, MAAF, MAAFs} such that
  HN: for computing the hybridization number;
  MAAF: for computing one MAAF and one optimal network;
  MAAFs: for computing all MAAFs and one optimal network for each MAAF;
while each of treeFile_1 and treeFile_2 contains a phylogenetic tree in Newick format such as (((1,4),3),2) and (((species1, species_3), cat),dog) ended with a semicolon (see below for two example trees). The name of each species must consist of letters in {a, ..., z, A, ..., Z, 0, ..., 9, _, .}. There is no limit on the length of the name of each species. Here are an example input tree and another one . You can view the trees using a simple JAVA application by my student Yohei Terazaki or Dendroscope by Daniel H. Huson.

If you like, you can also run the program as follows:
         program_name   treeFile_1   treeFile_2   OPTION   HEURISTIC
where HEURISTIC is a 3-bit binary string specifying the version of the program as follows.

• The first bit is 1 if and only if initial cluster reductions are adopted.
• The middle bit is 1 if and only if Heuristic 1 is adopted.
• The last bit is 1 if and only if Heuristic 2 is adopted.

• FastHN32.exe: Executable compiled under Windows XP (x86).
• FastHN.exe: Executable compiled under Windows 7 (x64).
• FastHN: Executable compiled under Linux.
• FastHNMac: Executable compiled under Mac OS.
• Two example input trees: T1.newick and T2.newick. The outputs: hybridization number, MAAF, MAAFs.
• The randomly generated datasets that have been used in our experiments.