Substitution Model - Neutral, Independent, Finite Sites Models

Neutral, Independent, Finite Sites Models

Most substitution models used to date are neutral, independent, finite sites models.

Neutral
Selection does not operate on the substitutions, and so they are unconstrained.
Independent
Changes in one site do not affect the probability of changes in another site.
Finite Sites
There are finitely many sites, and so over evolution, a single site can be changed multiple times. This means that, for example, if a character has value 0 at time 0 and at time t, it could be that no changes occurred, or that it changed to a 1 and back to a 0, or that it changed to a 1 and back to a 0 and then to a 1 and then back to a 0, and so on.

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