NAME

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

SYNOPSIS

         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();
         $rel->alignment($aln);
         $rel->tree($tree);
         my ($rc,$results) = $rel->run();

DESCRIPTION

       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 http://www.hyphy.org for more information.

       This module will generate the correct list of options for interfacing with
       TemplateBatchFiles/Ghostrides/Wrapper.bf.

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:

         http://redmine.open-bio.org/projects/bioperl/

AUTHOR - Albert Vilella

       Email avilella-at-gmail-dot-com

CONTRIBUTORS

       Additional contributors names and emails here

APPENDIX

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

   Default Values
       Valid and default values for REL are listed below.  The default values are always the
       first one listed.  These descriptions are essentially lifted from the python wrapper or
       provided by the author.

       INCOMPLETE DOCUMENTATION OF ALL METHODS

   new
        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

   run
        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]

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

   set_default_parameters
        Title   : set_default_parameters
        Usage   : $rel->set_default_parameters(0);
        Function: (Re)set the default parameters from the defaults
                  (the first value in each array in the
                   %VALIDVALUES class variable)
        Returns : none
        Args    : boolean: keep existing parameter values

Bio::Tools::Run::WrapperBase methods

   no_param_checks
        Title   : no_param_checks
        Usage   : $obj->no_param_checks($newval)
        Function: Boolean flag as to whether or not we should
                  trust the sanity checks for parameter values
        Returns : value of no_param_checks
        Args    : newvalue (optional)

   save_tempfiles
        Title   : save_tempfiles
        Usage   : $obj->save_tempfiles($newval)
        Function:
        Returns : value of save_tempfiles
        Args    : newvalue (optional)

   tempdir
        Title   : tempdir
        Usage   : my $tmpdir = $self->tempdir();
        Function: Retrieve a temporary directory name (which is created)
        Returns : string which is the name of the temporary directory
        Args    : none

   cleanup
        Title   : cleanup
        Usage   : $rel->cleanup();
        Function: Will cleanup the tempdir directory after a run
        Returns : none
        Args    : none

   io
        Title   : io
        Usage   : $obj->io($newval)
        Function:  Gets a L<Bio::Root::IO> object
        Returns : L<Bio::Root::IO>
        Args    : none