SYNOPSIS

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

DESCRIPTION

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

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

  [email protected]                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

[email protected]

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 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.

INCOMPLETE DOCUMENTATION OF ALL METHODS

new

 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

run

 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]

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   : $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

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   : $modeltest->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