###############################################################################
#
#  Aevol - An in silico experimental evolution platform
#
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# 
#  Aevol is a digital genetics model: populations of digital organisms are
#  subjected to a process of selection and variation, which creates a
#  Darwinian dynamics.
#  .
#  By modifying the characteristics of selection (e.g. population size,
#  type of environment, environmental variations) or variation (e.g.
#  mutation rates, chromosomal rearrangement rates, types of
#  rearrangements, horizontal transfer), one can study experimentally the
#  impact of these parameters on the structure of the evolved organisms.
#  In particular, since Aevol integrates a precise and realistic model of
#  the genome, it allows for the study of structural variations of the
#  genome (e.g. number of genes, synteny, proportion of coding sequences).
#  .
#  The simulation platform comes along with a set of tools for analysing
#  phylogenies and measuring many characteristics of the organisms and
#  populations along evolution.
#
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The complete documentation being quite heavy, it is not included in basic
distributions. Please visit www.aevol.fr


To take a quick tour, please take the following steps:

1) Compile Aevol with the following commands:
  cd aevol/build
  cmake ..
  make

In that process, you'll need development packages.
Here are the basic dependencies on a Debian system:
  build-essential
  cmake
  zlib1g-dev
  libboost-dev
  libx11-dev
  libboost-filesystem1.67-dev
One option to install them all at once is to run the following command:
sudo apt install build-essential cmake zlib1g-dev libboost-dev libx11-dev libboost-filesystem1.67-dev

2) To run an example, e.g. basic, assuming you're in Aevol's root directory:
  cd examples/basic
  ../../build/bin/aevol_create
  ../../build/bin/aevol_run

The first command will create an experiment with the parameters contained
in the "param.in" file
The second command will launch the simulation for 1000 generations
(otherwise, use the --nb_timesteps option to specify the desired number of
generations)

For more information, please see the manpages in the `doc` directory
(e.g. man -l aevol_create.1),
or run any executable with the --help option
(e.g. aevol_create --help),
and ultimately visit www.aevol.fr
