Programs for Computing MAAF, MAAFs, MAF, MAFs of Multiple Phylogenetic Trees
  After downloading a program, you can run it as follows:
         program_name   -OPTION   TreeFile
where OPTION is a string in the set {MAAF, MAAFs, MAF, MAFs} such that
  MAAF: for computing one MAAF and one network with the minimum number of reticulation vertices;
  MAAFs: for computing all MAAFs and one network with the minimum number of reticulation vertices for each MAAF;
  MAF: for computing one MAF;
  MAFs: for computing all MAFs;
while TreeFile contains two or more phylogenetic trees in Newick format such as (((1,4),3),2) and (((species1, species_3), cat),dog) ended with a semicolon. 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 is an example input file . You can view the trees using Dendroscope by Daniel H. Huson or a simple applet by my student Yohei Terazaki .

   If you run the programs with an option MAAF , the output will be one MAAF (represented by the leaf sets of the trees in the MAAF) together with an optimal network in the extended Newick format. If you run the programs with an option MAAFs , the output will be all MAAFs together with an optimal network in the extended Newick format for each MAAF. If you run the programs with an option MAF, the output will be one MAF (represented by the leaf sets of the trees in the MAF). If you run the programs with an option MAFs, the output will be all MAFs. You can view a network in the extended Newick format using Dendroscope by Daniel H. Huson.