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 |
|---|---|---|
| CHROMOSOME_INITIAL_LENGTH | \(5,000\) | Used only when no chromosome file is provided: initial length of the chromosome to generate |
| SEED | Seed used to initialize the random number | |
| GRID_SIZE | \(32 \times 32\) | Width and height of the world toroidal grid. It gives the total number of individuals and their geographic structure |
| 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 |
| MAX_INDEL_SIZE | 6 | Maximal size of the small deletions and small insertions |
| 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 |
| MIN_GENOME_LENGTH | \(1\) | Minimal acceptable length for a genome. Any mutation leading to a genome smaller than that value will be ignored |
| MAX_GENOME_LENGTH | \(10,000,000\) | Maximal acceptable length for a genome. Any mutation leading to a genome larger than that value will be ignored |
| DOSAGE_EFFECT | absolute | Specifies how the protein functions are combined and compared to the phenotypic target. In absolute mode the phenotype corresponds to the sum of the proteins’ effects. In relative mode, only the relative values of phenotypic traits with each other are considered. For Eukaryote Aevol, use relative. |
| MAX_TRIANGLE_WIDTH \(^{1}\) | \(0.033333333\) | Maximum width of the metabolic contribution of a gene to the phenotype (~level of pleiotropy) |
| ENV_ADD_GAUSSIAN | Add a Gaussian component to the phenotypic target | |
| ENV_ADD_TRIANGLE | Add a Triangle component to the phenotypic target | |
| 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_CONTROL | OFF | Whether to control the probability of autofecondation at the reproduction event, and if so, rate thereof |
| RECOMB_ON_ALIGN | OFF | Determine recombination breakpoints based on sequence alignments |
| ALIGN_FUNCTION | Function to compute the probability of recombination given an alignment score | |
| ALIGN_MATCH_BONUS | \(1\) | Increment to an alignment score for a match |
| ALIGN_MISMATCH_COST | \(-2\) | Decrement to an alignment score for a mismatch |