Provided by: libbio-perl-perl_1.6.901-2_all bug


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


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

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


       Convert a Bio::TreeIO to Pagel format.  More information here


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AUTHOR - Jason Stajich

       Email jason-at-bioperl-dot-org


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

        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)

        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

        Title   : next_tree
        Usage   :
        Example :
        Returns :
        Args    :

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