SIMPLE SOLUTIONS

AEVOL_PROPAGATE(1) - man page online | user commands

An in silico experimental evolution platform.

Chapter
July 2014
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)