Provided by: libbio-perl-run-perl_1.7.1-3_all bug


       Bio::Tools::Run::Phylo::Hyphy::REL - Wrapper around the Hyphy REL analysis


         use Bio::Tools::Run::Phylo::Hyphy::REL;
         use Bio::AlignIO;
         use Bio::TreeIO;

         my $alignio = Bio::AlignIO->new(-format => 'fasta',
                                         -file   => 't/data/hyphy1.fasta');

         my $aln = $alignio->next_aln;

         my $treeio = Bio::TreeIO->new(
             -format => 'newick', -file => 't/data/hyphy1.tree');

         my $rel = Bio::Tools::Run::Phylo::Hyphy::REL->new();
         my ($rc,$results) = $rel->run();


       This is a wrapper around the REL analysis of HyPhy ([Hy]pothesis Testing Using
       [Phy]logenies) package of Sergei Kosakowsky Pond, Spencer V. Muse, Simon D.W. Frost and
       Art Poon.  See for more information.

       This module will generate the correct list of options for interfacing with


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AUTHOR - Albert Vilella

       Email avilella-at-gmail-dot-com


       Additional contributors names and emails here


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

        Title   : valid_values
        Usage   : $factory->valid_values()
        Function: returns the possible parameters
        Returns:  an array holding all possible parameters. The default
       values are always the first one listed.  These descriptions are
       essentially lifted from the python wrapper or provided by the author.
        Args    : None

        Title   : new
        Usage   : my $obj = Bio::Tools::Run::Phylo::Hyphy::REL->new();
        Function: Builds a new Bio::Tools::Run::Phylo::Hyphy::REL object
        Returns : Bio::Tools::Run::Phylo::Hyphy::REL
        Args    : -alignment => the Bio::Align::AlignI object
                  -save_tempfiles => boolean to save the generated tempfiles and
                                     NOT cleanup after onesself (default FALSE)
                  -tree => the Bio::Tree::TreeI object
                  -params => a hashref of parameters (all passed to set_parameter)
                  -executable => where the hyphy executable resides

       See also: Bio::Tree::TreeI, Bio::Align::AlignI

        Title   : run
        Usage   : my ($rc,$results) = $rel->run($aln);
        Function: run the rel analysis using the default or updated parameters
                  the alignment parameter must have been set
        Returns : Return code, Hash
        Args    : L<Bio::Align::AlignI> object,
                L<Bio::Tree::TreeI> object [optional]

        Title   : create_wrapper
        Usage   : $self->create_wrapper
        Function: It will create the wrapper file that interfaces with the analysis bf file
        Example :
        Returns :
        Args    :