AEVOL(1) User Manual AEVOL(1)
/#test with man −l <file>
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)