This is not an answer but I am puzzled by your use of @indices. It contains the integers from 0 to 80 and is used in only one function

my @indices = (
    76, 46, 21, 15, 33, 20, 69, 65, 40, 11, 79, 22, 70, 43, 32, 30, 57
+, 19,
    39, 37, 62, 3,  4,  44, 51, 58, 25, 72, 64, 59, 48, 80, 42, 38, 61
+, 75,
    49, 1,  18, 71, 41, 2,  67, 13, 45, 60, 9,  7,  28, 6,  8,  54, 50
+, 73,
    56, 53, 77, 27, 16, 29, 52, 10, 24, 5,  26, 36, 23, 34, 31, 47, 14
+, 35,
    12, 55, 17, 0,  68, 74, 66, 78, 63
);                    #number of the columns.
...
sub genotype {
    my @seq;
    my @gene;
    my @string;
    push @gene, shuffle @indices;
    ...
}
[download]

this can be rewritten as

my $max_index = 80;
...
sub genotype {
    my @seq;
    my @gene = shuffle 0 .. $max_index;
    my @string;
    ...
}
[download]

which makes your intent clearer and avoids the possiblity of missing an integer.