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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 TemplateBatchFiles/Ghostrides/


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.                  - General discussion  - About the mailing lists


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

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:

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    :