use strict;
use warnings;

my $file1 = <<FILE;
dna:
species_1  ACCATGATACGATG
species_2  GGTTTCGACGCAGA
species_3  GGACTCAGCGACTA
FILE

my $file2 = <<FILE;
morph:
species_1  001001010201001001
species_2  002010200210120201
species_4  001001110000000101
species_5  111001001001000201
FILE

my %data;
my $dnaLen = 0;
my $morphLen = 0;

open IN, '<', \$file1 or die "Failed to open file1: $!";
while (<IN>) {
    next unless /(^\w+)\s+(\w+)/;
    $data{$1}{dna} = $2;
    $dnaLen ||= length $2;
}
close IN;

open IN, '<', \$file2 or die "Failed to open file2: $!";
while (<IN>) {
    next unless /(^\w+)\s+(\w+)/;
    $data{$1}{morph} = $2;
    $morphLen ||= length $2;
}
close IN;

die "No dna data found" unless $dnaLen;
die "No morph data found" unless $morphLen;

for my $species (sort keys %data) {
    $data{$species}{dna} ||= '?' x $dnaLen;
    $data{$species}{morph} ||= '?' x $morphLen;
    print "$species: $data{$species}{dna}$data{$species}{morph}\n";
}