gp_dimer records dinucleotide frequencies: in the simplest case -- frequencies of dimeres AA, AC, AG... ...TT. This is sometimes useful to characterize a sequence. You can also use it to see, what is the probability of finding a certain nucleotide N bases after another one, for example -- what is the frequency of an 'A' coming seven nucleotides after a 'T'. To set this distance, use the option -l.
All Genpak programs complain in situations you would also complain, like when they cannot find a sequence you gave them or the sequence is not valid.
The Genpak programs do not write over existing files. I have found this feature very useful :-)
I'm sure there are plenty left, so please mail me if you find them. I tried to clean up every bug I could find.
January Weiner III <email@example.com>