use Bio::Tools::Run::Phylo::LVB;

  # Create a SimpleAlign object.
  # NOTE. Aligning nucleotide sequence directly, as below, makes
  # sense for non-coding nucleotide sequence (e.g., structural RNA
  # genes, introns, ITS). For protein-coding genes, to prevent
  # Clustal intronducing frameshifts one should instead align the
  # translations of the genes, then convert the multiple alignment
  # to nucleotide by referring to the corresponding transcript
  # sequences (e.g., using EMBOSS tranalign).
  use Bio::Tools::Run::Alignment::Clustalw;
  $aln_factory = Bio::Tools::Run::Alignment::Clustalw->new(quiet => 1);
  $inputfilename = "/Users/daniel/nuc.fa";
  $aln = $aln_factory->align($inputfilename);

  # Create the tree or trees.
  $tree_factory = Bio::Tools::Run::Phylo::LVB->new(quiet => 1);
  @trees = $tree_factory->run($aln);

  # Or one can pass in a file name containing a nucleotide multiple
  # alignment in Phylip 3.6 format:
  $tree_factory = Bio::Tools::Run::Phylo::LVB->new(quiet => 1);
  $tree = $tree_factory->run("/Users/daniel/nuc.phy");

    # NOTE. The order of the members of @LVB_PARAMS is vital!
    @LVB_PARAMS = qw(FORMAT GAPS SEED DURATION BOOTSTRAPS);
    @OTHER_SWITCHES = qw(QUIET);
    foreach my $attr(@LVB_PARAMS, @OTHER_SWITCHES) {
        $OK_FIELD{$attr}++;

            return 'lvb';

    return undef;

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

    # set defaults
    $self->FORMAT("interleaved");
    $self->GAPS("unknown");
    $self->SEED("");
    $self->DURATION("slow");
    $self->BOOTSTRAPS(0);

    # re-set with user's values where specified
    my ($attr, $value);
    while (@args)  {
	$attr =   shift @args;
	$value =  shift @args;
	next if( $attr =~ /^-/ ); # don't want named parameters
        $self->$attr($value);	
    }
    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 ($self,$input) = @_;
    my ($infilename);

    # Create input file pointer
    $infilename = $self->_setinput($input);
    if (!$infilename) {$self->throw("Problems setting up for lvb. Probably bad input data in $input !");}
    
    # Create parameter string to pass to lvb program
    my $param_string = $self->_setparams();

    # run lvb
    my @trees = $self->_run($infilename,$param_string);

  return shift->run(@_);
}

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

    my ($self,$infile,$param_string) = @_;
    return unless(  $self->executable );

    my $instring;
    my $curpath = cwd;    
    unless( File::Spec->file_name_is_absolute($infile) ) {
	$infile = $self->io->catfile($curpath,$infile);
    }
    $instring =  $param_string;
    $self->debug( "Program ".$self->executable || ''."\n");

    # create LVB's working copy of the input file, which must be named "infile"
    # NOTE, we cut trailing spaces since they can cause trouble with LVB 2.1
    my $lvb_infile = $self->tempdir . "/infile";
    open(LVB_SUB_RUN_TMP_IN_FH, "$infile");
    open(LVB_SUB_RUN_TMP_OUT_FH, ">$lvb_infile");
    while (<LVB_SUB_RUN_TMP_IN_FH>) {
	s/ +$//;
        print LVB_SUB_RUN_TMP_OUT_FH
	    or $self->throw("output error on $lvb_infile");
    }
    chdir($self->tempdir);
    #open a pipe to run lvb to bypass interactive menus
    if ($self->quiet() || $self->verbose() < 0) {
    	open(LVB_PIPE,"|".$self->executable.">/dev/null");
    }
    else {
    	open(LVB_PIPE,"|".$self->executable);
    }
    print LVB_PIPE $instring;
    close(LVB_PIPE);	
    chdir($curpath);
    #get the results
    my $treefile = $self->tempdir . "/outtree";
    
    $self->throw("LVB did not create treefile correctly") 
  	unless (-e $treefile);

    #create the trees
    my $in  = Bio::TreeIO->new(-file => $treefile, '-format' => 'newick');
    my @trees = ();
    while (my $tree = $in->next_tree()) {
	push @trees, $tree;
    }

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

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

    # If $input is not a  reference it better be the name of a
    # file with the sequence/

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

    #  $input may be a SimpleAlign Object
    if ($input->isa("Bio::Align::AlignI")) {
        #  Open temporary file for both reading & writing of BioSeq array
	($tfh,$alnfilename) = $self->io->tempfile(-dir=>$self->tempdir);
	my $alnIO = Bio::AlignIO->new(-fh => $tfh, -format=>'phylip',idlength=>$10);
	$alnIO->write_aln($input);
	$alnIO->close();
	close($tfh);
	$tfh = undef;
	unless ($self->format() =~ /^interleaved$/i) {
	    $self->warn("resetting LVB format to interleaved");
	    $self->format("interleaved");
	}
	return $alnfilename;		
    }
    return 0;

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

    $self = shift;
    my $param_string = "";

    for $attr (@LVB_PARAMS) {
        $value = $self->$attr();
	if ($attr =~/SEED/i) {
	    $value = "" unless defined $value;
	    $param_string .= "$value\n";
	} elsif ($attr  =~ /BOOTSTRAPS/i) {
	    $value = 0 unless defined $value;
	    $param_string .= "$value\n";
	} else {	# we want I for "interleaved" or S for "sequential",
                        # U for "unknown" or F for "fifthstate",
			# F for "fast" or S for "slow"
	    $param_string .= uc(substr $value, 0, 1) . "\n";
	}
    }

    return $param_string;
}

1; # Needed to keep compiler happy

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

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

  Title       : FORMAT
  Description : (optional)
                When running LVB from a Phylip 3.6-format
                multiple alignment file, this specifies
                the layout of the file. It may be
                "interleaved" or "sequential". FORMAT is
                automatically set to "interleaved" if
                running from a SimpleAlign object.
                Defaults to "interleaved".

  Title       : GAPS
  Description : (optional)
                LVB can treat gaps represented in the
                multiple alignment by "-" as either
                "fifthstate" or "unknown". "fifthstate"
                regards "-" as equivalent to "O", which
                is an unambiguous character state
                distinct from all nucleotides. "unknown"
                regards "-" as equivalent to "?", which
                is as an ambiguous site that may contain
                "A" or "C" or "G" or "T" or "O".
                Defaults to "unknown".

  Title       : SEED
  Description : (optional)
                This specifies the random number seed
                for LVB. SEED must be an integer in the
                range 0 to 900000000 inclusive. If no
                seed is specified, LVB takes a seed from
                the system clock. By default, no seed is
                specified.

  Title       : DURATION
  Description : (optional)
                This specifies the duration of the
                analysis, which may be "fast" or "slow".
                "slow" causes LVB to perform a more
                thorough and more time-consuming search
                than "fast". Defaults to "slow".

  Title       : BOOTSTRAPS
  Description : (optional)
                This specifies the number of bootstrap
                replicates to use, which must be a
                positive integer. Set bootstraps to 0 for
                no bootstrapping. Defaults to 0.