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AEVOL(1)                                   User Manual                                   AEVOL(1)

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NAME
       aevol - an in silico experimental evolution platform

SYNOPSIS
       aevol_propagate -h or --help
       aevol_propagate -V or --version
       aevol_propagate [-v] [-g GENER] [-i INDIR] [-o OUTDIR] [-S GENERALSEED]
       aevol_propagate [-v] [-g GENER] [-i INDIR] [-o OUTDIR] [-s SELSEED] [-m MUTSEED] [-t
       STOCHSEED] [-e ENVVARSEED] [-n ENVNOISESEED]

DESCRIPTION
       Aevol is a simulation platform that allows one to let populations of digital organisms
       evolve in different conditions and study experimentally the mechanisms responsible for the
       structuration of the genome and the transcriptome.

       aevol_propagate
              creates a fresh copy of the experiment as it was at the given generation. The gen‐
              eration number of the copy will be reset to 0. If you use aevol_propagate repeat‐
              edly to initialize several simulations, you should specify a different seed for
              each simulation, otherwise all simulations will yield exactly the same results. You
              can use the option -S to do so. In this case, the random drawings will be different
              for all random processes enabled in your simulations (mutations, stochastic gene
              expression, selection, migration, environmental variation, environmental noise).
              Alternatively, to change the random drawings for specific random processes only, do
              not use -S but the options -m, -s, -t, -e, -n (see below).

OPTIONS
       -h, --help
              print help, then exit

       -V, --version
              print version number, then exit

       -v, --verbose
              be verbose

       -g, --gener GENER
              specify generation number (default: that contained in file last_gener.txt, if any)

       -i, --in INDIR
              specify input directory (default ".")

       -o, --out OUTDIR
              specify output directory (default "./output")

       -S, --general-seed GENERALSEED
              specify an integer to be used as a seed for random numbers. If you use aevol_propa‐
              gate repeatedly to initialize several simulations, you should specify a differ‐
              ent seed for each simulation, otherwise all simulations will yield exactly the same
              results. If you specify this general seed, random drawings will be different for
              all random processes enabled in your simulations (mutations, stochastic gene
              expression, selection, migration, environmental variation, environmental noise). To
              change the random drawings for a specific random process only, do not use -S but
              the options below.

       -s, --sel-seed SELSEED
              specify an integer as a seed for random numbers needed for selection and migration
              (if spatial structure is enabled).

       -m, --mut-seed MUTSEED
              specify an integer as a seed for random numbers needed for mutations.

       -t, --stoch-seed STOCHSEED
              specify an integer as a seed for random numbers needed for stochastic gene expres‐
              sion.

       -e, --env-var-seed ENVVARSEED
              specify an integer as a seed for random numbers needed for environmental variation.

       -n, --env-noise-seed ENVNOISESEED
              specify an integer as a seed for random numbers needed for environmental noise.

SEE ALSO
       aevol_create, aevol_run, aevol_modify

aevol 4.4                                   July 2014                                    AEVOL(1)