Provided by: libbio-perl-run-perl_1.7.2-4_all bug


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


         use Bio::Tools::Run::Phylo::Hyphy::FEL;
         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 $fel = Bio::Tools::Run::Phylo::Hyphy::FEL->new();
         my ($rc,$results) = $fel->run();


       This is a wrapper around the FEL 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 _

   Default Values
       Valid and default values for FEL 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.


        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::FEL->new();
        Function: Builds a new Bio::Tools::Run::Phylo::Hyphy::FEL object
        Returns : Bio::Tools::Run::Phylo::Hyphy::FEL
        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) = $fel->run($aln);
        Function: run the fel 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    :