Also, you might consider another type of data-structure, such as a hash, keyed by the value of the gene-string, whose value is the number of times that this particular string occurs.   This is remarkably easy to do in Perl:

my $h={};
$h->{ $_ } ++ foreach (@my_array);

After initializing $h to an empty hashref, we loop over all elements in @my_array (each element being briefly represented by the variable $_), and increment the value of the hash-entry under that key.   Welcome to Perl’s “auto-vivication” feature:   each hash-element is magically created as necessary, and since you are “incrementing” it, the initial value automagically starts at zero.

This representation is functionally-equivalent to an array of discrete strings, but much faster to process.