NAME

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

SYNOPSIS

         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/cysprot.stockholm';
         $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);

DESCRIPTION

       This is a wrapper for running the QuickTree application by Kevin Howe. You can download it
       here: http://www.sanger.ac.uk/Software/analysis/quicktree/

       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;

FEEDBACK

   Mailing Lists
       User feedback is an integral part of the evolution of this and other Bioperl modules. Send
       your comments and suggestions preferably to the Bioperl mailing list.  Your participation
       is much appreciated.

         bioperl-l@bioperl.org                  - General discussion
         http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

   Support
       Please direct usage questions or support issues to the mailing list:

       bioperl-l@bioperl.org

       rather than to the module maintainer directly. Many experienced and reponsive experts will
       be able look at the problem and quickly address it. Please include a thorough description
       of the problem with code and data examples if at all possible.

   Reporting Bugs
       Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their
       resolution. Bug reports can be submitted via the web:

         http://redmine.open-bio.org/projects/bioperl/

AUTHOR - Sendu Bala

       Email bix@sendu.me.uk

APPENDIX

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

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

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

   new
        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]

   upgma
        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.

   kimura
        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.

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

   run
        Title   : run
        Usage   : $factory->run($stockholm_file);
                  $factory->run($align_object);
        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).

   _setparams
        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

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