my $outfile = 'infile';

my @cmd = ("mafft", "--auto", "--phylipout", "--reorder", "$file.fasta" );

open my $out_fh, '>', $outfile 
  or die "open($outfile, w) failed: $!";

open( my $pipe, '-|', @cmd ) 
  or die sprintf "Could not open pipe from '%s': $!", join( ' ', @cmd);

while ( my $line =<$pipe> ) {
  print $out_fh $line
    or die "Write to '$outfile' failed: $!";
}

close $pipe;

close $out_fh or die "close($outfile) failed: $!";