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3.2. Initial Population

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ktheyss edited this page Jan 28, 2018 · 3 revisions

Element <population> in the Config File

The initial population is described by a population size and a way to create its genomes. Note that currently, the population size is kept constant throughout the entire simulation.

An example of a population definition:

<population>
    <populationSize>10000</populationSize>
    <inoculum>all</inoculum>
</population>

Population size: <populationSize>

The number of individuals in the population. Simulation speed is roughly N log N for a population size of N.

Inoculum: <inoculum>

Defines how the genomes for all individuals in the initial population are initialized. The

<inoculum>

definition is optional and 'none' is the default value.

Possible values are:

  • none: initialize the genome of all individuals to a default nucleotide sequence which is poly-adenine ('AAA...')

  • all: initialize the genome of each individual by sampling, with replacement, from all sequences provided in the <sequences> within the <genome> description.

  • consensus: initialize the genome of all individuals to the consensus sequence for the sequences provided in the <sequences> within the <genome> description.

  • random: initialize the genome of all individuals to the same sequence, randomly chosen from the sequences provided in the <sequences> within the <genome> description.

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