OK, this is a shot in the dark, but it's simple enough that it's worth trying. It's banking on the possibility that print_tree may be printing to the currently selected handle, as opposed to printing explicitly to STDOUT or to who knows what else:

my $str="catgatgttttccctatgggatttttgaa";
my $tree=create_tree($str);

my $filename7 = "C:\\MB\\Cp\\mississippi_out_7.txt";
open(MY7, ">>$filename7") or die "Unable to open $filename7: $!\n";

my $orig = select(MY7);
print_tree($tree);
select($orig);
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See select for more details. Note however that select is unusual in that it has two completely different meanings in Perl; here I'm using the select that operates on filehandles (obviously), not the one that operates on bit vectors.