Provided by: libbio-perl-run-perl_1.6.9-1_all bug


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


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


       This is a wrapper around the Modeltest 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 Modeltest 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   : new
        Usage   : my $obj = Bio::Tools::Run::Phylo::Hyphy::Modeltest->new();
        Function: Builds a new Bio::Tools::Run::Phylo::Hyphy::Modeltest object
        Returns : Bio::Tools::Run::Phylo::Hyphy::Modeltest
        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) = $modeltest->run($aln);
        Function: run the modeltest 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    :

        Title   : set_default_parameters
        Usage   : $modeltest->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

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

        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

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

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

perl v5.12.3                                2011-06-Bio::Tools::Run::Phylo::Hyphy::Modeltest(3pm)