In that case, you might find the concept of structured data useful.

my $data = {
    key1 => { label => "label1", content =>  [...] },
    key2 => ...,
};
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I actually have a hash set up already that contains keys= the labels and values= sequence content. I read these keys and values into an array because it was easier to manipulate them (reverse and tr them and insert spaces between characters). Is there a way to just manipulate them straight from a hash reference instead of putting the keys and values into arrays? If so, I can just avoid arrays all together

Of course you can manipulate the data. For example:

  foreach my $record (values %$HoH) {
     $record->{label} =~ tr/A-Za-z/N-ZA-Mn-za-m/;
  }
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Should perform the rot13 cryption on all the label fields. See perlop for =~, tr, etc.

my @order = sort { $labels[$a] cmp $labels[$b] } 0 .. $#labels;
@labels = @labels[@order];
@content = @content[@order];
@more_content = @more_content[@order];
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Yes, that was what I was getting at. Either this, or a hash or hashes, as shown by an anonymous monk just below.