Journal of Theoretical Biology 161(2) pp263-269 March 1993
School of Computer Science and Software Engineering,
Monash University, Australia 3168
It is shown how to normalize the costs of an alignment algorithm that
employs affine or linear gap costs. The normalized
costs are interpreted as the -log probabilities of
the instructions of a finite-state edit-machine.
This gives an explicit model relating sequences that can be linked to
processes of mutation and evolution.