If you are doing a multiple sequence alignment on 90 sequence, how many pairwise alignment need to be done?
This sounds very much like a course question and not an actual scientific problem.
It is a general question to understand the use of the tool.
90 * 89 / 2 = 4005
The Handshake Problem: in a room of n people, how many different handshakes are possible: n * (n-1) / 2
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