SYNOPSIS

use Bio::Tools::Run::Phylo::PAML::Yn00;
use Bio::AlignIO;
my $alignio = Bio::AlignIO->new(-format => 'phylip',
-file => 't/data/gf-s85.phylip');
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\n";
}

DESCRIPTION

This is a wrapper around the yn00 (method of Yang and Nielsen, 2000) program of PAML (Phylogenetic Analysis by Maximum Likelihood) package of Ziheng Yang. See http://abacus.gene.ucl.ac.uk/software/paml.html for more information.

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.

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:

AUTHOR - Jason Stajich

Email jason-at-bioperl.org

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

See the Bio::Tools::Run::Phylo::PAML::Codeml module for documentation of the default values.

program_name

 Title   : program_name
 Usage   : $yn00->program_name()
 Function: holds the program name
 Returns:  string
 Args    : None

program_dir

 Title   : program_dir
 Usage   : $yn00->program_dir()
 Function: returns the program directory, obtained from ENV variable.
 Returns:  string
 Args    :

new

 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)

run

 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

error_string

 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)

alignment

 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>

get_parameters

 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

set_parameter

 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()>

set_default_parameters

 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

Bio::Tools::Run::Wrapper methods

no_param_checks

 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)

save_tempfiles

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

outfile_name

 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

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   : $codeml->cleanup();
 Function: Will cleanup the tempdir directory after a PAML 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