## Normalization of Affine Gap Costs Used in Optimal Sequence Alignment

#### L. Allison, Journal of Theoretical Biology, 161(2), pp.263-269, doi:10.1006/jtbi.1993.1054, March 1993

**Abstract**:
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.

Paper here: [doi:10.1006/jtbi.1993.1054][4/'03], [preprint.ps].