Up: Deriving the Optimal Scoring
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Because our model of evolution is symmetrical, i.e. it does not
distinguish a particular sequence, E must be symmetric. It is
also easy to see that if we replace Eij by
then F(d) does not change (both numerator and denominator
are multiplied by ). Before we do any minimization we
have to eliminate these two degrees of freedom. Most of the time
this can be done by arbitrarily setting two values of E, e.g.
E11 = -1 and
E12 = 1.