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.\" ========================================================================
.\"
.IX Title "Bio::Tools::Run::Phylo::PAML::Yn00 3pm"
.TH Bio::Tools::Run::Phylo::PAML::Yn00 3pm "2020-11-10" "perl v5.32.0" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
.if n .ad l
.nh
.SH "NAME"
Bio::Tools::Run::Phylo::PAML::Yn00 \- Wrapper aroud the PAML program yn00
.SH "VERSION"
.IX Header "VERSION"
version 1.7.3
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 5
\&  use Bio::Tools::Run::Phylo::PAML::Yn00;
\&  use Bio::AlignIO;
\&  my $alignio = Bio::AlignIO\->new(\-format => \*(Aqphylip\*(Aq,
\&                        \-file   => \*(Aqt/data/gf\-s85.phylip\*(Aq);
\&  my $aln = $alignio\->next_aln;
\&
\&  my $yn = Bio::Tools::Run::Phylo::PAML::Yn00\->new();
\&  $yn\->alignment($aln);
\&  my ($rc,$parser) = $yn\->run();
\&  while( my $result = $parser\->next_result ) {
\&    my @otus = $result\->get_seqs();
\&    my $MLmatrix = $result\->get_MLmatrix();
\&    # 0 and 1 correspond to the 1st and 2nd entry in the @otus array
\&    my $dN = $MLmatrix\->[0]\->[1]\->{dN};
\&    my $dS = $MLmatrix\->[0]\->[1]\->{dS};
\&    my $kaks =$MLmatrix\->[0]\->[1]\->{omega};
\&    print "Ka = $dN Ks = $dS Ka/Ks = $kaks\en";
\&  }
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
This is a wrapper around the yn00 (method of Yang and Nielsen, 2000)
program of \s-1PAML\s0 (Phylogenetic Analysis by Maximum Likelihood) package
of Ziheng Yang.  See http://abacus.gene.ucl.ac.uk/software/paml.html
for more information.
.PP
This module will generate a proper yn00.ctl file and will run the
program in a separate temporary directory to avoid creating temp files
all over the place and will cleanup after itself.
.SS "Default Values"
.IX Subsection "Default Values"
See the Bio::Tools::Run::Phylo::PAML::Codeml module for
documentation of the default values.
.SH "ATTRIBUTES"
.IX Header "ATTRIBUTES"
.SS "program_name"
.IX Subsection "program_name"
.Vb 5
\& Title   : program_name
\& Usage   : $yn00\->program_name()
\& Function: holds the program name
\& Returns:  string
\& Args    : None
.Ve
.SS "program_dir"
.IX Subsection "program_dir"
.Vb 5
\& Title   : program_dir
\& Usage   : $yn00\->program_dir()
\& Function: returns the program directory, obtained from ENV variable.
\& Returns:  string
\& Args    :
.Ve
.SS "error_string"
.IX Subsection "error_string"
.Vb 5
\& Title   : error_string
\& Usage   : $obj\->error_string($newval)
\& Function: Where the output from the last analysus run is stored.
\& Returns : value of error_string
\& Args    : newvalue (optional)
.Ve
.SS "alignment"
.IX Subsection "alignment"
.Vb 8
\& Title   : alignment
\& Usage   : $codeml\->align($aln);
\& Function: Get/Set the L<Bio::Align::AlignI> object
\& Returns : L<Bio::Align::AlignI> object
\& Args    : [optional] L<Bio::Align::AlignI>
\& Comment : We could potentially add support for running directly on a file
\&           but we shall keep it simple
\& See also: L<Bio::SimpleAlign>
.Ve
.SS "no_param_checks"
.IX Subsection "no_param_checks"
.Vb 6
\& Title   : no_param_checks
\& Usage   : $obj\->no_param_checks($newval)
\& Function: Boolean flag as to whether or not we should
\&           trust the sanity checks for parameter values
\& Returns : value of no_param_checks
\& Args    : newvalue (optional)
.Ve
.SS "save_tempfiles"
.IX Subsection "save_tempfiles"
.Vb 5
\& Title   : save_tempfiles
\& Usage   : $obj\->save_tempfiles($newval)
\& Function:
\& Returns : value of save_tempfiles
\& Args    : newvalue (optional)
.Ve
.SS "outfile_name"
.IX Subsection "outfile_name"
.Vb 6
\& Title   : outfile_name
\& Usage   : my $outfile = $codeml\->outfile_name();
\& Function: Get/Set the name of the output file for this run
\&           (if you wanted to do something special)
\& Returns : string
\& Args    : [optional] string to set value to
.Ve
.SS "tempdir"
.IX Subsection "tempdir"
.Vb 5
\& 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
.Ve
.SH "METHODS"
.IX Header "METHODS"
.SS "new"
.IX Subsection "new"
.Vb 7
\& Title   : new
\& Usage   : my $obj = Bio::Tools::Run::Phylo::PAML::Yn00\->new();
\& Function: Builds a new Bio::Tools::Run::Phylo::PAML::Yn00 object
\& Returns : Bio::Tools::Run::Phylo::PAML::Yn00
\& Args    : \-alignment => the L<Bio::Align::AlignI> object
\&           \-save_tempfiles => boolean to save the generated tempfiles and
\&                              NOT cleanup after onesself (default FALSE)
.Ve
.SS "run"
.IX Subsection "run"
.Vb 12
\& Title   : run
\& Usage   : $yn\->run();
\& Function: run the yn00 analysis using the default or updated parameters
\&           the alignment parameter must have been set
\& Returns : 3 values,
\&           $rc = 1 for success, 0 for errors
\&           hash reference of the Yang calculated Ka/Ks values
\&                    this is a set of pairwise observations keyed as
\&                    sequencenameA\->sequencenameB\->datatype
\&           hash reference same as the previous one except it for the
\&           Nei and Gojobori calculated Ka,Ks,omega values
\& Args    : none
.Ve
.SS "get_parameters"
.IX Subsection "get_parameters"
.Vb 5
\& Title   : get_parameters
\& Usage   : my %params = $self\->get_parameters();
\& Function: returns the list of parameters as a hash
\& Returns : associative array keyed on parameter names
\& Args    : none
.Ve
.SS "set_parameter"
.IX Subsection "set_parameter"
.Vb 11
\& Title   : set_parameter
\& Usage   : $codeml\->set_parameter($param,$val);
\& Function: Sets a codeml parameter, will be validated against
\&           the valid values as set in the %VALIDVALUES class variable.
\&           The checks can be ignored if on turns of param checks like this:
\&             $codeml\->no_param_checks(1)
\& Returns : boolean if set was success, if verbose is set to \-1
\&           then no warning will be reported
\& Args    : $paramname => name of the parameter
\&           $value     => value to set the parameter to
\& See also: L<no_param_checks()>
.Ve
.SS "set_default_parameters"
.IX Subsection "set_default_parameters"
.Vb 7
\& Title   : set_default_parameters
\& Usage   : $codeml\->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
.Ve
.SS "cleanup"
.IX Subsection "cleanup"
.Vb 5
\& Title   : cleanup
\& Usage   : $codeml\->cleanup();
\& Function: Will cleanup the tempdir directory after a PAML run
\& Returns : none
\& Args    : none
.Ve
.SS "io"
.IX Subsection "io"
.Vb 5
\& Title   : io
\& Usage   : $obj\->io($newval)
\& Function:  Gets a L<Bio::Root::IO> object
\& Returns : L<Bio::Root::IO>
\& Args    : none
.Ve
.SH "Bio::Tools::Run::Wrapper methods"
.IX Header "Bio::Tools::Run::Wrapper methods"
.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/Support.html    \- About the mailing lists
.Ve
.SS "Support"
.IX Subsection "Support"
Please direct usage questions or support issues to the mailing list:
\&\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
\&  https://github.com/bioperl/bio\-tools\-phylo\-paml/issues
.Ve
.SH "AUTHOR"
.IX Header "AUTHOR"
Jason Stajich <jason@bioperl.org>
.SH "COPYRIGHT"
.IX Header "COPYRIGHT"
This software is copyright (c) by Jason Stajich <jason@bioperl.org>.
.PP
This software is available under the same terms as the perl 5 programming language system itself.