HGT-Gen: a tool for generating horizontal gene transferred phylogenetic tree

  • HGT-Gen is now available from here.

  • -> Link to PubMed

    Usage
    Input: HGT-Gen requires an input file containing the original phylogenetic tree in the Newick format. The time range (start and end) of the HGT events in relative evolutionary time and the number of the HGT trees in the output file are also required.
    Output: The output file contains the phylogenetic trees with HGT in the multi-Newick format.
    An example of the command: perl hgtgen.pl sample_input.tre 0.5 0.8 10 >output.tre

    Note
  • The relative evolutionary time at the root is 0, and that of OTU is 1.
  • End position must be equal or larger than the start position.
  • If the relative evolutionary time of "start position" is too small, HGT tree may not be created, because the topology of the tree may not changed after HGT. If all trees do not change the topology, output file will not be created.