I'm using Clustal Omega to calculate distance between RNA seq. I like to know if I can calculate only distance without making alignment?
I don't think it is possible. Anyway, why do you want to use an alignment program and not perform an alignment? There are programs devoted to distance calculation.
@h.mon Can you please tell me which ones are good?
You can find several alternatives here (note: not all perform distance calculations). I don't know which ones are "good" for distance calculation, but HyPhy, MEGA and Phylip are three very good packages for several aspects of phylogeny inference, including distance calculation.
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