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FastHN:A Fast Tool for Minimum Hybridization Networks  

2013-08-09 09:52:17|  分类: 生物信息分析 |  标签: |举报 |字号 订阅

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This site provides programs for computing 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   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.
Our experimental results show that one should choose HEURISTIC to be either 111 or 110.

The Programs, examples, and supplementary material: If you run the programs with an option HN , 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. You can view a network in the extended Newick format using Dendroscope by Daniel H. Huson.
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