Linear gap penalty ($g(\ell )=e\ell$)

A linear gap penalty assigns a cost proportional to gap length: $g(\ell )=e\ell$ for $e>0$. One gap of length three and three gaps of length one therefore incur the same total cost, before considering alignment substitutions. An affine gap penalty distinguishes opening from extending a gap and can favour fewer longer gaps. The chosen cost is part of the alignment model rather than an experimentally measured universal price of an insertion. ^[ref]