Alright, the last thing I have to ask is how I append the count to the end of each distinct line in the final output. As it stands right now, I get:

ALPHA:D 20 letters      ABCCEDFGGAACDDDEEEFG
ALPHA:D 20 letters      ABCCEDFFGAACDDDEEEFG
ALPHA:D 20 letters      ABCCEDFFGAACDDEEEEFG
ALPHA:E 24 letters      ABCCEDFFGAACDDDEEEFGAGAE
ALPHA:E 24 letters      ABCCEDFFGAACDDDEEEFGAGAD
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which is great! But I need to have the count of each distinct string, spaced by a tab... I'd like it to look like this:

ALPHA:D 20 letters      ABCCEDFGGAACDDDEEEFG   4
ALPHA:D 20 letters      ABCCEDFFGAACDDDEEEFG   3
ALPHA:D 20 letters      ABCCEDFFGAACDDEEEEFG   2
ALPHA:E 24 letters      ABCCEDFFGAACDDDEEEFGAGAE   7
ALPHA:E 24 letters      ABCCEDFFGAACDDDEEEFGAGAD   5
[download]

Is there an easy way to do this?

Yes, quite easy. For example:

for my $line (@sorted_data) {
     print "$line \t $hash_count{$line} \n";
}
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or:

print map {"$_ \t $hash_count{$_} \n"} @sorted_data;
[download]

Thanks! I think it should be "count_hash" instead of "hash_count", though. Before I read your post, I worked out this solution:

#!/usr/bin/perl -w
use strict;

my $file = "path to my file";
open (FH, "< $file") or die "Can't open $file for read: $!";
my @data = <FH>;
close FH or die "Cannot close $file: $!"; 
my %count_hash;
for my $line (@data) {
     $count_hash{$line} ++;
}
for my $line (sort { length $a <=> length $b || $count_hash{$b} <=> $c
+ount_hash{$a}} keys %count_hash) {
    print "$line\t$count_hash{$line}\n";
}
[download]

The only thing I see is that it seems to carry over the line break with each line, so the count ends up being on a new line, tabbed over. Is there a way to have it look for a line break and remove it before it prints>

Please disregard my final question. I just used "chomp" for each line, and got the results I wanted. Thanks again!