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";
  }

 
    $MINNAMELEN = 25;
    $PROGRAMNAME = 'yn00'  . ($^O =~ /mswin/i ?'.exe':'');
    if( defined $ENV{'PAMLDIR'} ) {
	$PROGRAM = Bio::Root::IO->catfile($ENV{'PAMLDIR'},$PROGRAMNAME);
    }
    # valid values for parameters, the default one is always
    # the first one in the array
    # much of the documentation here is lifted directly from the codeml.ctl
    # example file provided with the package
    %VALIDVALUES = ( 
		     'noisy'   => [ 0..3,9],
		     'verbose' => [ 0,1,2], # 0:concise, 1:detailed, 2:too much

		     'weighting' => [0,1], # weighting pathways between codons 
		     'commonf3x4' => [0,1], # use same f3x4 for all sites

		     # (icode) genetic code
		     # 0:universal code
		     # 1:mamalian mt
		     # 2:yeast mt
		     # 3:mold mt,
		     # 4:invertebrate mt
		     # 5:ciliate nuclear
		     # 6:echinoderm mt
		     # 7:euplotid mt
		     # 8:alternative yeast nu.
		     # 9:ascidian mt
		     #10:blepharisma nu
		     # these correspond to 1-11 in the genbank transl table
		     
		     'icode'    => [ 0..10], 
		     'ndata'    => [1..10],
		     );

    return $PROGRAMNAME;

            return Bio::Root::IO->catfile($ENV{PAMLDIR}) if $ENV{PAMLDIR};

  my($class,@args) = @_;

  my $self = $class->SUPER::new(@args);
  my ($aln,$st) = $self->_rearrange([qw(ALIGNMENT SAVE_TEMPFILES)],
				    @args);
  defined $aln && $self->alignment($aln);
  defined $st  && $self->save_tempfiles($st);
  
  $self->set_default_parameters();
  return $self;

   my ($self,$aln) = @_;
   ($aln) ||= $self->alignment();
   if( ! $aln ) { 
       $self->warn("must have supplied a valid alignment file in order to run yn00");
       return 0;
   }
   my ($tmpdir) = $self->tempdir();
   my ($tempseqFH,$tempseqfile);
   if( ! ref($aln) && -e $aln ) { 
       $tempseqfile = $aln;
   } else { 
       ($tempseqFH,$tempseqfile) = $self->io->tempfile
	   ('-dir' => $tmpdir, 
	    UNLINK => ($self->save_tempfiles ? 0 : 1));
       my $alnout = Bio::AlignIO->new('-format'      => 'phylip',
				     '-fh'          => $tempseqFH,
				     '-interleaved' => 0,
				     '-idlength'    => $MINNAMELEN > $aln->maxdisplayname_length() ? $MINNAMELEN : $aln->maxdisplayname_length() +1);
       
       $alnout->write_aln($aln);
       $alnout->close();
       undef $alnout;   
       close($tempseqFH);
       undef $tempseqFH;
   } 
   # now let's print the yn.ctl file.
   # many of the these programs are finicky about what the filename is 
   # and won't even run without the properly named file.  Ack
   
   my $yn_ctl = "$tmpdir/yn00.ctl";
   open(YN, ">$yn_ctl") or $self->throw("cannot open $yn_ctl for writing");
   print YN "seqfile = $tempseqfile\n";

   my $outfile = $self->outfile_name;

   print YN "outfile = $outfile\n";
   my %params = $self->get_parameters;
   while( my ($param,$val) = each %params ) {
       print YN "$param = $val\n";
   }
   close(YN);
   my ($rc,$parser) = (1);
   {
       my $cwd = cwd();
       my $exit_status;
       chdir($tmpdir);
       my $ynexe = $self->executable();
       $self->throw("unable to find executable for 'yn'") unless $ynexe;
       open(RUN, "$ynexe |");
       my @output = <RUN>;
       $exit_status = close(RUN);
       $self->error_string(join('',@output));
       if( (grep { /\berr(or)?: /io } @output) || !$exit_status ) {
	   $self->warn("There was an error - see error_string for the program output");
	   $rc = 0;
       }
       eval {
	   $parser = Bio::Tools::Phylo::PAML->new(-file => "$tmpdir/mlc", 
						 -dir => "$tmpdir");

       };
       if( $@ ) {
	   $self->warn($self->error_string);
       }
       chdir($cwd);
   }
   if( $self->verbose > 0 ) {
       open(IN, "$tmpdir/mlc");
       while(<IN>) {
	   $self->debug($_);
       }
   }
       
   unless ( $self->save_tempfiles ) {
      unlink("$yn_ctl");
      $self->cleanup();
   }
   return ($rc,$parser);

   my ($self,$value) = @_;
   if( defined $value) {
      $self->{'error_string'} = $value;
    }
    return $self->{'error_string'};

   my ($self,$aln) = @_;
   if( defined $aln ) { 
       if( !ref($aln) || ! $aln->isa('Bio::Align::AlignI') ) { 
	   $self->warn("Must specify a valid Bio::Align::AlignI object to the alignment function");
	   return undef;
       }
       $self->{'_alignment'} = $aln;
   }
   return  $self->{'_alignment'};

   my ($self) = @_;
   # we're returning a copy of this
   return %{ $self->{'_codemlparams'} };

   my ($self,$param,$value) = @_;
   if( ! defined $VALIDVALUES{$param} ) { 
       $self->warn("unknown parameter $param will not set unless you force by setting no_param_checks to true");
       return 0;
   } 
   if( ref( $VALIDVALUES{$param}) =~ /ARRAY/i &&
       scalar @{$VALIDVALUES{$param}} > 0 ) {
       
       unless ( grep {$value} @{ $VALIDVALUES{$param} } ) {
	   $self->warn("parameter $param specified value $value is not recognized, please see the documentation and the code for this module or set the no_param_checks to a true value");
	   return 0;
       }
   }
   $self->{'_codemlparams'}->{$param} = $value;
   return 1;

   my ($self,$keepold) = @_;
   $keepold = 0 unless defined $keepold;
   
   while( my ($param,$val) = each %VALIDVALUES ) {
       # skip if we want to keep old values and it is already set
       next if( defined $self->{'_codemlparams'}->{$param} && $keepold);
       if(ref($val)=~/ARRAY/i ) {
	   $self->{'_codemlparams'}->{$param} = $val->[0];
       }  else { 
	   $self->{'_codemlparams'}->{$param} = $val;
       }
   }

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

 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)

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

 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

 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

 Title   : cleanup
 Usage   : $codeml->cleanup();
 Function: Will cleanup the tempdir directory after a PAML run
 Returns : none
 Args    : none

 Title   : io
 Usage   : $obj->io($newval)
 Function:  Gets a Bio::Root::IO object
 Returns : Bio::Root::IO
 Args    : none