Bio::Tools::Run::Phylo::Forester::SDI my $runner = Bio::Tools::Run::Phylo::Forester::SDI->new(); # run with file $runner->species_tree_file('tree_of_life_bin_1-4.nhx'); $runner->gene_tree_file('input_tree.nhx') ; $runner->output_file('out.tree'); $runner->run_file; This wrapper is for SDI in Forester package. For more details on Forester, please see http://www.genetics.wustl.edu/eddy/forester/

NOTE
You have to do something before running this module, since SDI will popup a GUI window to visualize the structure of the result treee, which is not expected by someone who only want the result file. You need to comment out the source code to popup the window on the main method of class forester.tools.SDI . Then recompile it and make it accessible in CLASSPATH Juguang Xiao, juguang at tll.org.sg This module is a free software. You may copy or redistribute it under the same terms as Perl itself.