File#1
dna:
species_1  ACCATGATACGATG
species_2  GGTTTCGACGCAGA
species_3  GGACTCAGCGACTA

File#2
morph:
species_1  001001010201001001
species_2  002010200210120201
species_4  001001110000000101
species_5  111001001001000201

##</code><code>##

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

##</code><code>##

open IN, "dnamorph.txt" or die $!;
my %data;
my $taxon;
while (<IN>) {
	if (/(^\w+)(\t+)(\w+)/) {
		$taxon = $1;
		push @{ $data{$taxon} }, $3;
	}
}

##</code><code>##

species_1  ACCATGATACGATG001001010201001001
species_2  GGTTTCGACGCAGA002010200210120201
species_3  GGACTCAGCGACTA
species_4  001001110000000101
species_5  111001001001000201

##</code><code>##

open DNAA, "dna.nxs" or die $!;
my %ddata;
while (<DNAA>) {
	if (/(^\w+)(\t+)(\w+)/) {
		$ddata{ $1} = {
			dna => $3,
		};
	}
}

##</code><code>##

species_six: dna=TTGGGACAGCCGAGGCACGA 
species_two: dna=AAAATCGGGCGGCGCTTTTC 
species_five: dna=TTCCAGGACATCGGCATACG 
species_three: dna=GGGGCCCCAATATCGATACG 
species_four: dna=GGGGAGGACGTAGATATTAT 
species_one: dna=ACTGTTTCGTAGGGCTAGGA 

species_two: morph=111101011011011 
species_five: morph=111101011011011 
species_three: morph=012111011011011 
species_four: morph=112111011011011 
species_one: morph=110111011011111