compseq counts the composition of dimer/trimer/etc words in a sequence.
Here is a sample session with compseq. To count the frequencies of dinucleotides in a file:
% compseq embl:hsfau 2 result3.comp
To count the frequencies of hexanucleotides, without outputting the results of hexanucleotides that do not occur in the sequence:
% compseq embl:hsfau 6 result6.comp -nozero
To count the frequencies of trinucleotides in frame 2 of a sequence using a previously prepared compseq output to show the expected frequencies:
% compseq embl:hsfau 3 result3.comp -frame 2 -in prev.comp
Optional qualifiers (bold if not always prompted):