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File#1
dna:
...
species_2  002010200210120201
species_4  001001110000000101
species_5  111001001001000201

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species_1  ACCATGATACGATG001001010201001001
species_2  GGTTTCGACGCAGA002010200210120201
species_3  GGACTCAGCGACTA??????????????????
species_4  ??????????????001001110000000101
species_5  ??????????????111001001001000201

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open IN, "dnamorph.txt" or die $!;
my %data;
...
        push @{ $data{$taxon} }, $3;
    }
}

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species_1  ACCATGATACGATG001001010201001001
species_2  GGTTTCGACGCAGA002010200210120201
species_3  GGACTCAGCGACTA
species_4  001001110000000101
species_5  111001001001000201

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open DNAA, "dna.nxs" or die $!;
my %ddata;
...
        };
    }
}

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species_six: dna=TTGGGACAGCCGAGGCACGA 
species_two: dna=AAAATCGGGCGGCGCTTTTC 
...
species_three: morph=012111011011011 
species_four: morph=112111011011011 
species_one: morph=110111011011111