3.4. Replication

Element <replicator> in the Config File

The replicator defines how a child genome is created given one or more parent genomes.

Two different replication operators are available. A clonal replicator copies the genome from a single parent. A recombinant replicator considers that occasionally a child genome is derived from two parents, where the child genome sequence is created by copying the genome of one or the other parent, switching between these two genomes at random sites. In both cases, occasional mistakes during the copying are modelled by the mutation operator <mutator>.

Clonal replication: <clonalReplicator>

The clonal replicator simply copies the genome of a single parent. It has no parameters that need to be defined.

An example of a clonal replicator:

<replicator>
    <clonalReplicator />
</replicator>

Recombinant replication: <recombinantReplicator>

The recombinant replicator considers that occasionally a child genome is derived from two parents, where the child genome sequence is created by copying the genome of one or the other parent, switching between these two genomes at random sites.

The operator is configured using two parameters. The first parameter (<dualInfectionProbability>) defines the probability that recombination takes place, and its name is based on the replication model of HIV where recombination can only occur when a single cell was infected simultaneously by two different virions, in this way packaging two different genomes in a single virion. The second parameter (<recombinationProbability>) defines the probability (per nucleotide site) that recombination occurs, switching between these two template genomes.

An example of a recombinant replicator:

<replicator>
    <recombinantReplicator>
        <dualInfectionProbability>0.05</dualInfectionProbability>
	<recombinationProbability>0.001</recombinationProbability>
    </recombinantReplicator>
</replicator>

The parameters are:

• <dualInfectionProbability> : the probability that a child genome should be derived from two parent genomes, using the recombination process, instead of being derived from a single parent genome using clonal replication.

• <recombinationProbability> : the probability per site that a recombination event happens while copying the genome.