The name popped into CN's head when someone asked him some six years ago what his program was called. He thinks the Q must have come from the common use of the letter to mean an unknown quantity or a mystery, as well as from the Qs in quantitative (as in QTL) and qualitative genetics.
As for the logo, that was created about three years ago when, needing a program icon, he noticed that the curly bit on a Q could be made into a turn of a DNA helix. That's what we're asking Qs about and doing Q genetics upon. The two double helices correspond with the DNA replication step that precedes meiotic pairing and crossing over, the cell events on which these investigations depend.
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