NAME

       Bio::TreeIO::pag - Bio::TreeIO driver for Pagel format

SYNOPSIS

         use Bio::TreeIO;
         my $in = Bio::TreeIO->new(-format => 'nexus',
                                   -file   => 't/data/adh.mb_tree.nexus');

         my $out = Bio::TreeIO->new(-format => 'pag');
         while( my $tree = $in->next_tree ) {
           $out->write_tree($tree);
         }

DESCRIPTION

       Convert a Bio::TreeIO to Pagel format.  More information here
       http://www.evolution.reading.ac.uk/index.html

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://github.com/bioperl/bioperl-live/issues

AUTHOR - Jason Stajich

       Email jason-at-bioperl-dot-org

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::TreeIO::pag->new();
        Function: Builds a new Bio::TreeIO::pag object
        Returns : an instance of Bio::TreeIO::pag
        Args    : -file/-fh for filename or filehandles
                  -name_length for minimum name length (default = 10)

   write_tree
        Title   : write_tree
        Usage   :
        Function: Write a tree out in Pagel format
                  Some options are only appropriate for bayesianmultistate and
                  the simpler output is only proper for discrete
        Returns : none
        Args    : -no_outgroups => (number)
                  -print_header => 0/1 (leave 0 for discrete, 1 for bayesianms)
                  -special_node => special node - not sure what they wanted to do here
                  -keep_outgroup => 0/1 (keep the outgroup node in the output)
                  -outgroup_ancestor => Bio::Tree::Node (if we want to exclude or include the outgroup this is what we operate on)
                  -tree_no       => a tree number label - only useful for BayesianMultistate

   next_tree
        Title   : next_tree
        Usage   :
        Function:
        Example :
        Returns :
        Args    :

   name_length
        Title   : name_length
        Usage   : $self->name_length(20);
        Function: set minimum taxon name length
        Returns : integer (length of name)
        Args    : integer