Provided by: libbio-perl-perl_1.7.2-2_all bug


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


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


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

       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 bootstrap 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'.


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AUTHOR - Jason Stajich

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


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

        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

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

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

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

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