Aevol Programs
When compiling Aevol, you get a whole bunch different programs (a.k.a binaries), which can be unsettling.
The first thing to understand is that these programs come in 3 families, corresponding to the three flavors of Aevol: Standard, Eukaryote and 4-Bases.
The flavor a program corresponds to can be identified by its suffix as follows:
| Program Suffix | Aevol Flavor |
|---|---|
| _2b | Standard |
| _4b | 4-Bases |
| _eukaryote_2b | Eukaryote |
Aevol is primarily made of 2 main programs to create and run simulations. After simulations have been run, they can be analysed using post-mortem analysis tools
| Program | Explanation | User doc |
|---|---|---|
| aevol_create | Create a new simulation from provided parameters | aevol_create |
| aevol_run | Run a simulation | aevol_run |
Aevol comes with a set of analysis tools to help understand what happened during evolution:
| Program | Explanation | User doc |
|---|---|---|
| aevol_post_lineage | Reconstruct the lineage of a given individual | aevol_post_lineage |
| aevol_post_ancestor_stats | Compute statistics on ancestry described in lineage file | aevol_post_ancestor_stats |
| aevol_post_extract_genomes | Extract genome(s) in fasta format from aevol checkpoints | aevol_post_extract_genomes |
| aevol_post_mutagenesis | Generate single-mutants of the provided individuals | aevol_post_mutagenesis |
| aevol_post_replicative_robustness | Generate offsprings of the provided individuals | aevol_post_replicative_robustness |
Aevol also provide some tools (although quite raw) for visualizing data from a simulation.
The basic workflow is to generate json data files and then feed these files to a python script that will generate views in SVG format.
The json data files used for visualization can be generated on the fly during a run using the --ui-output-frequency argument (and optionally --ui-output-dir) from aevol_run
If you want to generate these files after a simulation has run, you can use one of the following:
| Program | Explanation | User doc |
|---|---|---|
| aevol_post_make_ui_output_from_checkpoint | Generate visualization output files from aevol checkpoints | |
| aevol_post_make_ui_output_from_fasta | Generate visualization output files from from fasta and parameter file |
Once you have your json data you can use the aevol_ui_build_views python script (get it with pip install aevol) to generate visualizations from your data
| Script | Explanation | User doc |
|---|---|---|
| aevol_ui_build_views | Create graphical views from the provided input |