## Finite-State Models in the Alignment of Macro-Molecules.

#### L.Allison, C.S.Wallace & C.N.Yee, J. Molec. Evol., 35(1), pp.77-89, 1992

**Abstract**:
Minimum message length encoding is a technique of
inductive inference with theoretical and practical advantages.
It allows the posterior odds-ratio of two theories or hypotheses
to be calculated.
Here it is applied to problems of aligning
or relating two strings, in particular
two biological macro-molecules.
We compare the *r-theory*, that the strings are *related*,
with the null-theory, that they are not related.
If they are related, the probabilities of the various alignments
can be calculated.
This is done for one, three and five-state models of relation or mutation.
These correspond to linear and piece-wise linear cost functions
on runs of insertions and deletions.
We describe how to estimate parameters of a model.
The validity of a model is itself an hypothesis and can
be objectively tested.
This is done on real DNA strings and on artificial data.
The tests on artificial data indicate limits on what can be
inferred in various situations.
The tests on real DNA support either the three or five-state models
over the one-state model.
Finally, a fast, approximate, minimum message length string
comparison algorithm is described.

[doi:10.1007/BF00160262], or [paper.ps] and [software].

Also see on phylogenetic [trees & multiple alignment].