use Tie::File;

...

tie my @seq_data, 'Tie::File', $sequence_fname
    or die "Can't open $sequence_fname: $!";

if(!($permute)){
    for (@seq_data) {
        my @line = split /\t/;
        ...
    }
    ...
{
else{
    open(OUT,">>$out")||die "Cannot open $out\n";

    for (...) {
        ...
        for (@seq_data) {
            my @line = split /\t/;
            ...
        }

        foreach my $key(keys %ktc){
            ...
            print OUT ...
            ...
        }
    }

    close OUT;
}

untie @seq_data;