Initialize a simulation (aevol_create)

Warning

Any new simulation must be run in a new directory.

aevol_create comes in three flavors:

aevol_create_2b for Standard Aevol
aevol_create_4b for 4-Bases Aevol
aevol_create_eukaryote_2b for Eukaryote Aevol

Using aevol_create to initialize a simulation:

There are two main ways to initialize a simulation:

from scratch, using a randomly generated initial genome
from a provided sequence (usually a WildType)

From scratch

When creating a new simulation from scratch, a simple bootstrapping method is used to generate the initial genome: genomes whose corresponding fitness is lower than that of a genome with no genes are discarded. This implies that the generated genome codes for at least one beneficial gene.

aevol_create_2b parameter_file.in

For Eukaryote Aevol, it's advised to start from a haploid organism

and perform a whole genome duplication. The initialisation of a diploid from scratch often results in the loss of the diploidy.

From a WildType

Note that example sequence files with pre-evolved organisms and their associated parameter files are provided in the example directory in the GitLab, as well as on the dedicated WildTypes page.

aevol_create_2b parameter_file.in --fasta sequence_file.fa

This is the only recommended way of starting a Eukaryote experiment. The provided fasta file should already be diploid. Generally, this can be achieved by duplicating the single chromosome of a haploid fasta file (evolved with the Standard Aevol). Note that in this case, the DOSAGE_EFFECT option should be set to relative (otherwise the phenotype would be doubled).

Usage of aevol_create (output of `aevol_create --help`)

aevol_create: create an experiment with setup as specified in PARAM_FILE.

Usage : aevol_create -h or --help
   or : aevol_create -V or --version
   or : aevol_create [PARAM_FILE] [--fasta SEQ_FILE]

Options
  -h, --help
	print this help, then exit
  -V, --version
	print version number, then exit
  --fasta SEQUENCE_FILE
	load sequences from given file (in fasta format) instead of generating it