...

my @species = sort keys %data;
my $nSpecies = @species;

# Print the header
print "begin data;\n";
printf "dimensions ntax=%d nchar=%d;\n", $nSpecies, $dnaLen + $morphLen;
printf "format datatype=mixed (dna:1-%d, standard:%d-%d)  missing=? gap=-;\n",
    $dnaLen, $dnaLen + 1, $dnaLen + $morphLen;
print "Matrix\n";

# Print the data
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";
}

print "end;\n";