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.IX Title "Bio::Tools::Run::Phylo::Hyphy::REL 3pm"
.TH Bio::Tools::Run::Phylo::Hyphy::REL 3pm "2023-01-22" "perl v5.36.0" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
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.SH "NAME"
Bio::Tools::Run::Phylo::Hyphy::REL \- Wrapper around the Hyphy REL analysis
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 3
\&  use Bio::Tools::Run::Phylo::Hyphy::REL;
\&  use Bio::AlignIO;
\&  use Bio::TreeIO;
\&
\&  my $alignio = Bio::AlignIO\->new(\-format => \*(Aqfasta\*(Aq,
\&                                  \-file   => \*(Aqt/data/hyphy1.fasta\*(Aq);
\&
\&  my $aln = $alignio\->next_aln;
\&
\&  my $treeio = Bio::TreeIO\->new(
\&      \-format => \*(Aqnewick\*(Aq, \-file => \*(Aqt/data/hyphy1.tree\*(Aq);
\&
\&  my $rel = Bio::Tools::Run::Phylo::Hyphy::REL\->new();
\&  $rel\->alignment($aln);
\&  $rel\->tree($tree);
\&  my ($rc,$results) = $rel\->run();
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
This is a wrapper around the \s-1REL\s0 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.
.PP
This module will generate the correct list of options for interfacing
with TemplateBatchFiles/Ghostrides/Wrapper.bf.
.SH "FEEDBACK"
.IX Header "FEEDBACK"
.SS "Mailing Lists"
.IX Subsection "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.
.PP
.Vb 2
\&  bioperl\-l@bioperl.org                  \- General discussion
\&  http://bioperl.org/wiki/Mailing_lists  \- About the mailing lists
.Ve
.SS "Support"
.IX Subsection "Support"
Please direct usage questions or support issues to the mailing list:
.PP
\&\fIbioperl\-l@bioperl.org\fR
.PP
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.
.SS "Reporting Bugs"
.IX Subsection "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:
.PP
.Vb 1
\&  http://redmine.open\-bio.org/projects/bioperl/
.Ve
.SH "AUTHOR \- Albert Vilella"
.IX Header "AUTHOR - Albert Vilella"
Email avilella-at-gmail-dot-com
.SH "CONTRIBUTORS"
.IX Header "CONTRIBUTORS"
Additional contributors names and emails here
.SH "APPENDIX"
.IX Header "APPENDIX"
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
.SS "valid_values"
.IX Subsection "valid_values"
.Vb 7
\& 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
.Ve
.SS "new"
.IX Subsection "new"
.Vb 10
\& Title   : new
\& Usage   : my $obj = Bio::Tools::Run::Phylo::Hyphy::REL\->new();
\& Function: Builds a new Bio::Tools::Run::Phylo::Hyphy::REL object
\& Returns : Bio::Tools::Run::Phylo::Hyphy::REL
\& Args    : \-alignment => the Bio::Align::AlignI object
\&           \-save_tempfiles => boolean to save the generated tempfiles and
\&                              NOT cleanup after onesself (default FALSE)
\&           \-tree => the Bio::Tree::TreeI object
\&           \-params => a hashref of parameters (all passed to set_parameter)
\&           \-executable => where the hyphy executable resides
.Ve
.PP
See also: Bio::Tree::TreeI, Bio::Align::AlignI
.SS "run"
.IX Subsection "run"
.Vb 7
\& Title   : run
\& Usage   : my ($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]
.Ve
.SS "create_wrapper"
.IX Subsection "create_wrapper"
.Vb 6
\& Title   : create_wrapper
\& Usage   : $self\->create_wrapper
\& Function: It will create the wrapper file that interfaces with the analysis bf file
\& Example :
\& Returns :
\& Args    :
.Ve