After executing the script, a Tree in newick form is generated (form a fasta file given). How can I output this result into a file and not just leave it in my command promt? Thanks!

#!/usr/bin/perl

$ENV{CLUSTALDIR} = 'C:\\\\\\\\\\\\\\\\\\\\;
use Bio::Tools::Run::Alignment::Clustalw;

my $file = <>; # Get file name (fasta file) from command prompt.

#  Build a clustalw alignment factory
my $factory = Bio::Tools::Run::Alignment::Clustalw->new(-matrix => 'BL
+OSUM',-outfile=>'out', -output =>'clustalw'); 
my $ktuple = 2;
$factory->ktuple($ktuple);

my $inseq = Bio::SeqIO->new(
                    -file=> "<$file",
                    -format=> 'fasta'
                   );
my $seq;
my @seq_array;
while ($seq = $inseq->next_seq) {
    push(@seq_array, $seq);
}
# Now we do the actual alignment.
my $seq_array_ref = \@seq_array;
my $aln = $factory->align($seq_array_ref);

#constarcting the Tree
my $alnio = Bio::AlignIO->new(-file => 'out', -format=>'clustalw');

my $dfactory = Bio::Tree::DistanceFactory->new(-method => 'NJ');

my $stats = Bio::Align::ProteinStatistics->new;

my $treeout = Bio::TreeIO->new(-format => 'newick');

while( my $aln = $alnio->next_aln ) 
{
 my $mat = $stats->distance(-method => 'Kimura',
                            -align  => $aln);
 my $tree = $dfactory->make_tree($mat);
 $treeout->write_tree($tree);
}

exit;

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In reply to how to output the final Tree into a file? by dimitris852

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