Software for Computing Hybridization Networks

Software for Computing rSPR Distances, Hybridization Numbers, and Hybridization Networks

   This site provides programs for computing the rSPR distance , a maximum agreement forest (MAF) , all maximum agreement forests (MAFs) , the hybridization number , a maximum acyclic agreement forest (MAAF) , or all maximum acyclic agreement forests (MAAFs) of two given phylogenetic trees. Once our programs find an MAAF, they also construct an optimal hybridization network .
  After downloading a program, you can run it as follows:
         program_name -OPTION treeFile_1 treeFile_2
where OPTION is a string in the set {HN, MAAF, MAAFs, rSPRDist, MAF, MAFs} 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;
rSPRDist: for computing the rSPR distance;
MAF: for computing one MAF;
MAFs: for computing all MAFs;
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.

The Programs, examples, and supplementary material:

HybridNet32.exe: Executable compiled under Windows XP (x86).
HybridNet.exe: Executable compiled under Windows 7 (x64).
HybridNet: Executable compiled under Linux.
HybridNetMac: Executable compiled under Mac OS.
Two example input trees: T1.newick and T2.newick. The outputs: hybridization number, MAAF, MAAFs, rSPR distances, MAF, MAFs.
Supplementary material.

If you run the programs with an option HN or rSPRDist , the output will just be a number. 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.