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, the initialisation phase has to be done with the 'relative dosage' phenotype computation option

Otherwise, this will result in a population of individuals having a single functional chromosome and the other one empty. This is due to dosage imbalance when duplicating the first genes and a strong founding effect.

From a WildType

Note that example sequence files with pre-evolved organisms are provided in the example directory.

aevol_create_2b parameter_file.in --fasta sequence_file.fa

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