Provided by: libbio-perl-run-perl_1.7.1-3_all bug


       Bio::Tools::Run::Phylo::QuickTree - Wrapper for rapid reconstruction of
                                           phylogenies using QuickTree


         use Bio::Tools::Run::Phylo::QuickTree;

         #  Make a QuickTree factory
         @params = ();
         $factory = Bio::Tools::Run::Phylo::QuickTree->new(@params);

         #  Pass the factory an alignment
         $inputfilename = 't/data/';
         $tree = $factory->run($inputfilename); # $tree is a Bio::Tree::Tree object.
         # or get a Bio::Align::AlignI (SimpleAlign) object from somewhere
         $tree = $factory->run($aln);


       This is a wrapper for running the QuickTree application by Kevin Howe. You can download it

       Currently only input with alignments and output of trees is supported. (Ie.  no support
       for distance matrix in/out.)

       You will need to enable this QuickTree wrapper to find the quicktree program.  This can be
       done in (at least) three ways:

        1. Make sure the QuickTree executable is in your path.
        2. Define an environmental variable QUICKTREEDIR which is a
           directory which contains the 'quicktree' application:
           In bash:

           export QUICKTREEDIR=/home/username/quicktree_1.1/bin

           In csh/tcsh:

           setenv QUICKTREEDIR /home/username/quicktree_1.1/bin

        3. Include a definition of an environmental variable QUICKTREEDIR in
           every script that will use this QuickTree wrapper module, e.g.:

           BEGIN { $ENV{QUICKTREEDIR} = '/home/username/quicktree_1.1/bin' }
           use Bio::Tools::Run::Phylo::QuickTree;


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AUTHOR - Sendu Bala



       The rest of the documentation details each of the object methods.  Internal methods are
       usually preceded with a _

        Title   : program_name
        Usage   : $factory>program_name()
        Function: holds the program name
        Returns : string
        Args    : None

        Title   : program_dir
        Usage   : $factory->program_dir(@params)
        Function: returns the program directory, obtained from ENV variable.
        Returns : string
        Args    : None

        Title   : new
        Usage   : $factory = Bio::Tools::Run::Phylo::QuickTree->new(@params)
        Function: creates a new QuickTree factory
        Returns : Bio::Tools::Run::Phylo::QuickTree
        Args    : Optionally, provide any of the following (default in []):
                  -upgma  => boolean # Use the UPGMA method to construct the tree [0]
                  -kimura => boolean # Use the kimura translation for pairwise
                                     # distances [0]
                  -boot   => int     # Calculate bootstrap values with n iterations [0]

        Title   : upgma
        Usage   : $factory->upgma(1);
        Function: Choose to use the UPGMA method to construct the tree.
        Returns : boolean (default 0)
        Args    : None to get, boolean to set.

        Title   : kimura
        Usage   : $factory->kimura(1);
        Function: Choose to use the kimura translation for pairwise distances.
        Returns : boolean (default 0)
        Args    : None to get, boolean to set.

        Title   : boot
        Usage   : $factory->boot(100);
        Function: Choose to calculate bootstrap values with the supplied number of
        Returns : int (default 0)
        Args    : None to get, int to set.

        Title   : run
        Usage   : $factory->run($stockholm_file);
        Function: Runs QuickTree to generate a tree
        Returns : Bio::Tree::Tree object
        Args    : file name for your input alignment in stockholm format, OR
                  Bio::Align::AlignI compliant object (eg. Bio::SimpleAlign).

        Title   : _setparams
        Usage   : Internal function, not to be called directly
        Function: Creates a string of params to be used in the command string
        Returns : string of params
        Args    : none

        Title   : _writeAlignFile
        Usage   : obj->_writeAlignFile($seq)
        Function: Internal(not to be used directly)
        Returns : filename
        Args    : Bio::Align::AlignI