@trips = join(" ", @trips);

##</code><code>##

#!/usr/bin/env perl 
use strict;
use warnings;
use List::Util 'shuffle';

print "enter sequence and signal end with enter followed by ctrl d\n";
my $sequence = <STDIN>;
chomp $sequence;
print "sequence inserted : $sequence\n";
my @trips = unpack("a3" x (length($sequence)-2), $sequence);
my @shuffled = shuffle(@trips);
print "@shuffled\n";

##</code><code>##

$ perl /tmp/shuf.pl 
enter sequence and signal end with enter followed by ctrl d
aaabbbcccddd
sequence inserted : aaabbbcccddd
ccc aaa    ddd  bbb