NAME

       Bio::Tree::Draw::Cladogram - Drawing phylogenetic trees in Encapsulated PostScript (EPS)
       format.

SYNOPSIS

         use Bio::Tree::Draw::Cladogram;
         use Bio::TreeIO;
         my $treeio = Bio::TreeIO->new('-format' => 'newick',
                                      '-file'   => 'input.nwk');
         my $t1 = $treeio->next_tree;
         my $t2 = $treeio->next_tree;

         my $obj1 = Bio::Tree::Draw::Cladogram->new(-tree => $t1);
         $obj1->print(-file => 'cladogram.eps');

         if ($t2) {
           my $obj2 = Bio::Tree::Draw::Cladogram->new(-tree => $t1, -second => $t2);
           $obj2->print(-file => 'tanglegram.eps');
         }

DESCRIPTION

       Bio::Tree::Draw::Cladogram is a Perl tool for drawing Bio::Tree::Tree objects in
       Encapsulated PostScript (EPS) format. It can be utilized both for displaying a single
       phylogenetic tree (a cladogram) and for the comparative display of two phylogenetic trees
       (a tanglegram) such as a gene tree and a species tree, a host tree and a parasite tree,
       two alternative trees for the same set of taxa, or two alternative trees for overlapping
       sets of taxa.

       Phylogenetic trees are drawn as rectangular cladograms, with horizontal orientation and
       ancestral nodes centered over their descendents. The font used for taxa is Courier at 10
       pt. A single Bio::Tree::Tree object is drawn with ancestors to the left and taxa flushed
       to the right. Two Bio::Tree::Tree objects are drawn with the first tree oriented left-to-
       right and the second tree oriented right-to-left, and with corresponding taxa connected by
       straight lines in a shade of gray. Each correspondence between a $taxon1 of the first tree
       and a $taxon2 of the second tree is established by setting
       $taxon1->add_tag_value('connection',$taxon2). Thus, a taxon of the first tree can be
       connected to more than one taxon of the second tree, and vice versa.

       The branch from the parent to a child $node, as well as the child label, can be colored by
       setting $node->add_tag_value('Rcolor',$r), $node->add_tag_value('Gcolor',$g), and
       $node->add_tag_value('Bcolor',$b), where $r, $g, and $b are the desired values for red,
       green, and blue (zero for lowest, one for highest intensity).

       This is a preliminary release of Bio::Tree::Draw::Cladogram. Future improvements include
       an option to output phylograms instead of cladograms. Beware that cladograms are
       automatically scaled according to branch lengths, but the current release has only been
       tested with trees having unit branch lengths.

       The print method could be extended to output graphic formats other than EPS, although
       there are many graphics conversion programs around that accept EPS input. For instance,
       most Linux distributions include epstopdf, a Perl script that together with Ghostscript,
       converts EPS to PDF.

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:

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

AUTHOR - Gabriel Valiente

       Email valiente@lsi.upc.edu

       Code for coloring branches contributed by Georgii A Bazykin (gbazykin@princeton.edu).

APPENDIX

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

   new
        Title   : new
        Usage   : my $obj = Bio::Tree::Draw::Cladogram->new();
        Function: Builds a new Bio::Tree::Draw::Cladogram object
        Returns : Bio::Tree::Draw::Cladogram
        Args    : -tree => Bio::Tree::Tree object
                  -second => Bio::Tree::Tree object (optional)
                  -font => font name [string] (optional)
                  -size => font size [integer] (optional)
                  -top => top margin [integer] (optional)
                  -bottom => bottom margin [integer] (optional)
                  -left => left margin [integer] (optional)
                  -right => right margin [integer] (optional)
                  -tip => extra tip space [integer] (optional)
                  -column => extra space between cladograms [integer] (optional)
                  -compact => ignore branch lengths [boolean] (optional)
                  -ratio => horizontal to vertical ratio [integer] (optional)
                  -colors => use colors to color edges [boolean] (optional)
                  -bootstrap => draw bootstrap or internal ids [boolean]

   print
        Title   : print
        Usage   : $obj->print();
        Function: Outputs $obj in Encapsulated PostScript (EPS) format
        Returns :
        Args    : -file => filename (optional)