3.5. Mutation

Element <mutator> in the Config File

The mutation operator describes the probability that errors are made while creating a new genome.

The nucleotide mutation operator: <nucleotideMutator>

The nucleotide mutation operator describes the mutation process as a Poisson process that acts on individual sites. A mutation bias may be specified either by specifying a bias for transitions versus transversions, or by specifying the relative rate for all 12 possible mutations.

An example of a nucleotide mutation operator:

<mutator>
    <nucleotideMutator>
        <mutationRate>1.0E-4</mutationRate>
        <transitionBias>2.0</transitionBias>
    </nucleotideMutator>
</mutator>

The parameters are:

• <mutationRate> : the probability for a mutation to occur (per site and per generation)

• <transitionBias> : a relative preference for transitions versus transversions

• <rates> : instead of specifying a transition bias, you can provide a white-space separated list of all 12 relative rates: A->C A->G A->T C->A C->G C->T G->A G->C G->T T->A T->C T->G