#Create a SimpleAlign object
  @params = ('ktuple' => 2, 'matrix' => 'BLOSUM');
  $factory = Bio::Tools::Run::Alignment::Clustalw->new(@params);
  $inputfilename = 't/data/cysprot.fa';
  $aln = $factory->run($inputfilename); # $aln is a SimpleAlign object.

  # Create the Distance Matrix
  # using a default PAM matrix and id name lengths limit of 30 note to
  # use id name length greater than the standard 10 in neighbor, you
  # will need to modify the neighbor source code

  $protdist_factory = Bio::Tools::Run::Phylo::Phylip::ProtDist->new(@params);
  my $matrix  = $protdist_factory->run($aln);

  #Create the tree passing in the distance matrix
  @params = ('type'=>'NJ','outgroup'=>2,'lowtri'=>1,
             'upptri'=>1,'subrep'=>1);

  my $neighbor_factory = 
     Bio::Tools::Run::Phylo::Phylip::Neighbor->new(@params);

  #you can set your outgroup using either a number specifying
  #the rank in the matrix or you can just use the name of the
  #species

  $neighbor_factory->outgroup('ENSP00001');
  #or
  $neighbor_factory->outgroup(1);

  my ($tree) = $neighbor_factory->run($matrix);

  # Alternatively, one can create the tree by passing in a file name 
  # containing a phylip formatted distance matrix(using protdist)
  my $neighbor_factory = 
    Bio::Tools::Run::Phylo::Phylip::Neighbor->new(@params);
  my ($tree) = $neighbor_factory->run('/home/shawnh/prot.dist');

  # To prevent PHYLIP from truncating sequence names:
  # Step 1. Shelf the original names:
    my ($aln_safe, $ref_name)=                    #   $aln_safe has serial names
               $aln->set_displayname_safe();      #   $ref_name holds original names
  # Step 2. Run ProtDist and Neighbor:
    $matrix  = $protdist_factory->
                creat_distance_matrix($aln_safe); #  Use $aln_safe instead of $aln
    $tree = $neighbor_factory->run($matrix);
  # Step 3. Retrieve orgininal OTU names:
    use Bio::Tree::Tree;
    my @nodes=$tree->get_nodes();
    foreach my $nd (@nodes){
       $nd->id($ref_name->{$nd->id_output}) if $nd->is_Leaf;
    }

    $PROGRAMNAME="neighbor";
    if (defined $ENV{PHYLIPDIR}) {
	$PROGRAMDIR = $ENV{PHYLIPDIR} || '';
	$PROGRAM = Bio::Root::IO->catfile($PROGRAMDIR,
					  $PROGRAMNAME.($^O =~ /mswin/i ?'.exe':''));
    }
    else {
	$PROGRAM = $PROGRAMNAME;
    }
	@NEIGHBOR_PARAMS = qw(TYPE OUTGROUP LOWTRI UPPTRI SUBREP JUMBLE MULTIPLE);
	@OTHER_SWITCHES = qw(QUIET);
	foreach my $attr(@NEIGHBOR_PARAMS,@OTHER_SWITCHES) {
		$OK_FIELD{$attr}++;

  return 'neighbor';

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

    my ($class,@args) = @_;
    my $self = $class->SUPER::new(@args);

    my ($attr, $value);
    while (@args)  {
	$attr =   shift @args;
	$value =  shift @args;
	next if( $attr =~ /^-/ ); # don't want named parameters
	if ($attr =~ /IDLENGTH/i){
		$self->idlength($value);
		next;
	}
	$self->$attr($value);	
    }
    if (! defined $self->idlength){
	$self->idlength(10);
    }
    return $self;

    my $self = shift;
    my $attr = $AUTOLOAD;
    $attr =~ s/.*:://;
    $attr = uc $attr;
    $self->throw("Unallowed parameter: $attr !") unless $OK_FIELD{$attr};
    $self->{$attr} = shift if @_;
    return $self->{$attr};

   my $self = shift;
   if( @_ ) {
      my $value = shift;
      $self->{'idlength'} = $value;
    }
    return $self->{'idlength'};

    my ($self,$input) = @_;
    my ($temp,$infilename, $seq);
    my ($attr, $value, $switch);
# Create input file pointer
    $infilename = $self->_setinput($input);
    if (!$infilename) {$self->throw("Problems setting up for neighbor. Probably bad input data in $input !");}

# Create parameter string to pass to neighbor program
    my $param_string = $self->_setparams();

# run neighbor
    my @tree = $self->_run($infilename,$param_string);
    return wantarray ? @tree:\@ tree;

  return shift->run(@_);
}


#################################################

    my ($self,$infile,$param_string) = @_;
    my $instring;
    my $curpath = cwd;    
    unless( File::Spec->file_name_is_absolute($infile) ) {
	$infile = $self->io->catfile($curpath,$infile);
    }
    $instring =  $infile."\n$param_string";
    $self->debug( "Program ".$self->executable."\n");
    chdir($self->tempdir);
	#open a pipe to run neighbor to bypass interactive menus
    if ($self->quiet() || $self->verbose() < 0) {
	open(NEIGHBOR,"|".$self->executable.">/dev/null");
    }
    else {
	open(NEIGHBOR,"|".$self->executable);
    }
    print NEIGHBOR $instring;
    close(NEIGHBOR);	
    chdir($curpath);
    #get the results
    my $outfile = $self->io->catfile($self->tempdir,$self->outfile);
    my $treefile = $self->io->catfile($self->tempdir,$self->treefile);
    
    $self->throw("neighbor did not create tree correctly (expected $treefile) ") unless (-e $treefile);
    my $in  = Bio::TreeIO->new(-file => $treefile, '-format' => 'newick');
    my @tree;
    while (my $tree = $in->next_tree){
        push @tree, $tree;
    }

    # Clean up the temporary files created along the way...
    unless ( $self->save_tempfiles ) { 
	unlink $outfile;
	unlink $treefile;
    }
    return @tree;

    my ($self, $input) = @_;
    my ($alnfilename,$infilename, $temp, $tfh,$input_tmp,$input_fh);

    #If $input is not a  filename it better be a HASF reference 

    #  a phy formatted alignment file created by protdist 
    unless (ref $input) {
	# check that file exists or throw
  	$alnfilename= $input;
   	unless (-e $input) {return 0;}
    	return $alnfilename;
    }

    my @input = ref($input) eq "ARRAY" ? @{$input} : ($input);
    ($tfh,$alnfilename) = $self->io->tempfile(-dir=>$self->tempdir);
    my $input_count = 0;
    foreach my $input(@input){
    	if ($input->isa("Bio::Matrix::PhylipDist")){
	     #  Open temporary file for both reading & writing of distance matrix
	     print $tfh $input->print_matrix;
       $input_count++;
	    }
    }
    $self->_input_nbr($input_count);
    close($tfh);
    #get names from the first matrix, to be used in outgroup ordering
    my %names;
    $input = shift @input;
    #set the species names
    my @names = @{$input->names};
    for(my $i=0; $i<= $#names; $i++){
	$names{$names[$i]} = $i+1;
    }
    $self->names(\%names);
    return $alnfilename;

    my ($self,$val) = @_;
    if($val){
        $self->{'_input_nbr'} = $val;
    }    return $self->{'_input_nbr'};

    my ($self,$name) = @_;
    if($name){
        $self->{'_names'} = $name;
    }
    return $self->{'_names'};

    my ($attr, $value, $self);

    #do nothing for now
    $self = shift;
    my $param_string = "";
    my $type ="";
    my $version = $self->version;
    my %menu = %{$Menu{$version}->{'NEIGHBOR'}};

    foreach  my $attr ( @NEIGHBOR_PARAMS) {
    	$value = $self->$attr();
    	next unless (defined $value && $value);
  	  if ($attr =~/TYPE/i){
	     if ($value=~/UPGMA/i){
    		$type = "UPGMA";
    		$param_string .= $menu{'TYPE'}{'UPGMA'};
       }
	    }
    	elsif($attr =~ /OUTGROUP/i){
	      if ($type ne "UPGMA"){
          if($value !~/^\d+$/){ # is a name so find the rank 
              my %names = %{$self->names};
              $names{$value} || $self->throw("Outgroup $value not found");
              $value = $names{$value};
          }
      		$param_string .= $menu{'OUTGROUP'}."$value\n";
	      }
	       else {
        		$self->throw("Can't set outgroup using UPGMA. Use Neighbor-Joining instead");
	       }
    	}
	    elsif ($attr =~ /JUMBLE/i){
	     $self->throw("Unallowed value for random seed, need odd number") unless ($value =~ /\d+/ && ($value % 2 == 1));
	     $param_string .=$menu{'JUMBLE'}."$value\n";
	    }
      elsif($attr=~/MULTIPLE/i){
        $param_string.=$menu{'MULTIPLE'}."$value\n";
        #version 3.6 needs a random seed
        if($version eq "3.6"){
            $param_string .= (2 * int(rand(10000)) + 1)."\n";
        }
      }
    	else{
       $param_string .= $menu{uc $attr};
	    }
    } 
   if (($param_string !~ $menu{'MULTIPLE'}) && (defined ($self->_input_nbr) &&($self->_input_nbr > 1))){
  $param_string.=$menu{'MULTIPLE'}.$self->_input_nbr."\n";
    }
 
    $param_string .=$menu{'SUBMIT'};

    return $param_string;

  Title 	: TYPE
  Description	: (optional)
                  This sets the type of tree to construct, using
                  neighbor joining or UPGMA.

		  NJ	Neighbor Joining
		  UPGMA	UPGMA

  Usage         : @params = ('type'=>'X');#where X is one of the values above
		  Defaults to NJ 

 		  For more information on the usage of the different
                  models, please refer to the documentation found in
                  the phylip package.

  Title		: OUTGROUP 
  Description	: (optional)
                  This option selects the species to be used as the outgroup
  Acceptable Values: integer 
  Usage         : @params = ('outgroup'=>'X'); 
                  where X is an positive integer not more than the 
                  number of sequences 
		  Defaults to 1

  Title		: LOWTRI
  Description   : (optional)
                  This indicates that the distance matrix is 
                  input  in  Lower-triangular form  (the  lower-left 
		  half of the distance matrix only, without the zero 
		  diagonal elements)
  Usage         : @params = ('lowtri'=>'X'); where X is either 1 or 0 
		  Defaults to 0

  Title         : UPPTRI 
  Description   : (optional)
                  This indicates that the distance matrix is input  in  
                  upper-triangular form  (the  upper-right half of the 
		  distance matrix only, without the zero diagonal elements.)
Usage           : @params = ('upptri'=>'X'); where X is either 1 or 0 
                  Defaults to 0

  Title         : SUBREP 
  Description   : (optional)
                  This is the Subreplication option.  

		  It informs the program that after each distance will
		  be provided an integer indicating that the distance
		  is a mean of that many replicates.

  Usage         : @params = ('subrep'=>'X'); where X is either 1 or 0 
                  Defaults to 0

  Title        : JUMBLE 
  Description  : (optional)

                 This enables you to tell the program to use a random
                 number generator to choose the input order of
                 species.  seed: an integer between 1 and 32767 and of
                 the form 4n+1 which means that it must give a
                 remainder of 1 when divided by 4.  Each different
                 seed leads to a different sequence of addition of
                 species.  By simply changing the random number seed
                 and re-running programs one can look for other, and
                 better trees.  iterations:

  Usage        : @params = ('jumble'=>'17); where 17 is the random seed
                 Defaults to no jumble

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

  http://redmine.open-bio.org/projects/bioperl/

 Title   : outfile
 Usage   : $obj->outfile($newval)
 Function: Get/Set default PHYLIP outfile name ('outfile' usually)
 Returns : value of outfile
 Args    : newvalue (optional)

 Title   : treefile
 Usage   : $obj->treefile($newval)
 Function: Get/Set the default PHYLIP treefile name ('treefile' usually)
 Returns : value of treefile
 Args    : newvalue (optional)