my $seq=(keys %SEQ)[$j]   <--- missing semicolon
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Question: What will (keys %SEQ)[$j] return the next time?
Answer: (this space intentionally filled with nonsense)

If you want to iterate over the keys of a hash, get a list of them and iterate over this list:

    for(my $i=1; $i<@aas; $i++){
        my $aa = $aas[$i];
        @codons = @{$Deg_codons{$aa}};
        my @SEQ = keys %SEQ;
        my $s = scalar @SEQ;
        for(my $j=0;$j<$s;$j++){
            my $seq=@SEQ[$j];
            foreach my $codon(@codons){
                $SEQ{$seq.$codon}=1;
                $j++;
                $s++;
            }
            delete $SEQ{$seq};
            $j--;
            $s--;
        }
    }
[download]

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                              /\_¯/(q    /
----------------------------  \__(m.====·.(_("always off the crowd"))."·
");sub _{s./.($e="'Itrs `mnsgdq Gdbj O`qkdq")=~y/"-y/#-z/;$e.e && print}