NAME

       Bio::TreeIO::nexus - A TreeIO driver module for parsing Nexus tree output from PAUP

SYNOPSIS

         use Bio::TreeIO;
         my $in = Bio::TreeIO->new(-file => 't/data/cat_tre.tre');
         while( my $tree = $in->next_tree ) {
         }

DESCRIPTION

       This is a driver module for parsing PAUP Nexus tree format which basically is just a
       remapping of trees.

   Comments
       The nexus format allows node comments that are placed inside square brackets. Usually the
       comments (implemented as tags for nodes) are used to give a name for an internal node or
       record the bootstap value, but other uses are possible.

       The FigTree program by Andrew Rambaut adds various rendering parameters inside comments
       and flags these comments by starting them with '&!'. The parameters implemented here are
       'label' and 'color'.

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 - Jason Stajich

       Email jason-at-open-bio-dot-org

APPENDIX

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

   new
        Title   : new
        Args    : -header    => boolean  default is true
                                print/do not print #NEXUS header
                  -translate => boolean default is true
                                print/do not print Node Id translation to a number

   next_tree
        Title   : next_tree
        Usage   : my $tree = $treeio->next_tree
        Function: Gets the next tree in the stream
        Returns : Bio::Tree::TreeI
        Args    : none

   write_tree
        Title   : write_tree
        Usage   : $treeio->write_tree($tree);
        Function: Writes a tree onto the stream
        Returns : none
        Args    : Bio::Tree::TreeI

   header
        Title   : header
        Usage   : $obj->header($newval)
        Function:
        Example :
        Returns : value of header (a scalar)
        Args    : on set, new value (a scalar or undef, optional)

   translate_node
        Title   : translate_node
        Usage   : $obj->translate_node($newval)
        Function:
        Example :
        Returns : value of translate_node (a scalar)
        Args    : on set, new value (a scalar or undef, optional)