Thanks GrandFather. Very helpful. Sorry to have been a bit light on context. I am trying to put DNA sequence data and coded morphological data into a file format that is accepted by a number of programs that reconstruct the evolutionary relationships amongst a group of organisms. The file will look something like this: 
#nexus

begin data;
    dimensions ntax=5 nchar=32;
    format datatype=mixed (dna:1-14, standard:15-32)  missing=? gap=-;
Matrix
species_1: ACCATGATACGATG001001010201001001
species_2: GGTTTCGACGCAGA002010200210120201
species_3: GGACTCAGCGACTA??????????????????
species_4: ??????????????001001110000000101
species_5: ??????????????111001001001000201
end;

[download]
The number of species and characters can be quite large.

In reply to Re^2: Combining hashes of hahses? by erio
in thread Combining hashes of hahses? by erio

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