3.9. Example Config Files

Several examples of simulation config files could be found on the project page, where all the described features of the software could be explored.

Here we dissect one of these examples in detail:

small.xml:

. The number of replicates is set to one using the element <replicates>1</replicates>.

. Inside the <genome> element the length of genome is introduced with the element <length>9</length>.

. In this case the population starts with only one unique sequence which is the same for all the individuals. This starting sequence is introduced using the element <sequences> GAAGAAGAG </sequences>. One could choose to introduce several sequences here or use the sequences from a fasta file.

. A protein coding <feature> named CDS is defined for all the 9 DNA positions.

. Population size is introduced using the element <populationSize>1000</populationSize>. Since there is no entry specifying dynamic population size inside the <population> element, constant population size is assumed.

. In the <fitnessFunction> element two fitness functions are defined. <neutralFitness> function is applied on the sites 1 to 9. Since no feature is declared, these are DNA coordinates. <purifyingFitness> is defined on the 1st site of CDS feature. Since CDS feature is defined with amino acid type, the coordinates of <purifyingFitness> corresponds to protein sites.

. <mutationRate> is defined within the <nucleotideMutator> element.

. Inside the <replicator> element clonal replicator or recombinant replicator could be introduced. In this case <clonalReplicator> is introduced.

. Number of generations in set inside the <epoch> element. One could introduce several consecutive epochs with different fitness functions or mutation rates for different number of generations.