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#1
#!/usr/bin/perl
...
# Now we do the actual alignment.
my $seq_array_ref = \@seq_array;
my $aln = $factory->align($seq_array_ref);

#2
my $alnio = Bio::AlignIO->new('-file'=> 'out_file','-format' => 'clust
+alw');

...
 my $tree = $dfactory->make_tree($mat);
 $treeout->write_tree($tree);
}