Parameters
To run a simulation, you will generally want to provide a parameter file to specify the experimental conditions for the run (it is also possible to use default parameters, but this is not recommended).
A parameter file consists of one keyword parameter per line with its arguments, separated by spaces. Additional comments should be preceded with a # sign.
Examples are provided in the example directory: example directory on the GitLab.
| Parameter name | Default value(s) | Description |
|---|---|---|
| SEED | \(5,000\) | Seed used to initialize the random number generators |
| WORLD_SIZE | \(32 \times 32\) | Width and height of the world toroidal grid. It gives the total number of individuals and their geographic structure |
| CHROMOSOME_INITIAL_LENGTH | \(5,000\) | Used only when no chromosome file is provided: initial length of the chromosome to generate |
| SELECTION_SCOPE | local \(3 \times 3\) | Type of selection scope (local or global), and in case of a local selection, width and height of the patch on which the local competition is done |
| SELECTION_SCHEME | fitness_proportionate 1000 | Selection method and associated parameter |
| POINT_MUTATION_RATE | \(5 \times 10^{-5}\) | Per base substitution rate |
| SMALL_INSERTION_RATE | \(5 \times 10^{-5}\) | Per base small insertion rate |
| SMALL_DELETION_RATE | \(5 \times 10^{-5}\) | Per base small deletion rate |
| DUPLICATION_RATE | \(5 \times 10^{-5}\) | Per base duplication rate |
| DELETION_RATE | \(5 \times 10^{-5}\) | Per base deletion rate |
| TRANSLOCATION_RATE | \(5 \times 10^{-5}\) | Per base translocation rate |
| INVERSION_RATE | \(5 \times 10^{-5}\) | Per base inversion rate |
| MAX_INDEL_SIZE | 6 | Maximal size of the small deletions and small insertions |
| ENV_ADD_GAUSSIAN | Add a Gaussian component to the phenotypic target | |
| MAX_TRIANGLE_WIDTH \(^{1}\) | \(0.033333333\) | Maximum width of the metabolic contribution of a gene to the phenotype (~level of pleiotropy) |
| CHECKPOINT_STEP | \(1,000\) | Interval between 2 checkpoints |
| RECORD_TREE | ON \(1,000\) | Whether to record the genealogical trees (containing all the mutational events) and at which interval |
| STATS_BEST | ON \(1\) | Whether to record statistics about the best individual and at which interval |
| STATS_POP | ON \(1\) | Whether to record statistics about the whole population and at which interval |
(1): Note that MAX_TRIANGLE_WIDTH is a scaling factor for the \(w\) parameter of a protein (see this section of the model description)
Some parameters are specific to Eukaryote Aevol:
| Parameter name | Default value(s) | Description |
|---|---|---|
| SELFING_RATE | \(0\) | Probability of autofecondation at the reproduction event |
| ALIGN_SCORE | Minimal alignment score to find to perform a meiotic recombination |