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\chapternonum{Appendix : Man Pages}
\label{app:manpages}
\addcontentsline{toc}{chapter}{Appendix : Man Pages}
\section{aevol\_create}
\label{sec:aevol-create}
\subsection*{Synopsis}
\begin{verbatim}
aevol_create -h or --help
aevol_create -V or --version
aevol_create [-f param_file]
\end{verbatim}
\subsection*{Description}
Create an experiment with setup as specified in param\_file.
\subsection*{Options}
\begin{verbatim}
-h, --help
print this help, then exit
-V, --version
print version number, then exit
-f, --file param_file
specify parameter file (default: param.in)
\end{verbatim}
\newpage
\section{aevol\_run}
\label{sec:aevol-run}
\subsection*{Synopsis}
\begin{verbatim}
aevol_run -h | --help
aevol_run -V | --version
aevol_run [-r GENER] [-n NB_GENER] [-tvwx]
\end{verbatim}
\subsection*{Description}
Run an \aevol{} simulation.
\subsection*{Options}
\begin{verbatim}
-h, --help
print this help, then exit
-V, --version
print version number, then exit
-r, --resume GENER
specify generation to resume simulation at (default 0)
-n, --nbgener NB_GENER
specify number of generations to be run (default 1000)
-t, --text
use text files instead of binary files when possible
-v, --verbose
be verbose
\end{verbatim}
\newpage
\section{aevol\_propagate}
\label{sec:aevol-propagate}
\subsection*{Synopsis}
\begin{verbatim}
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]
\end{verbatim}
\subsection*{Description}
\verb?aevol_propagate? creates a fresh copy of the experiment as it was at the given generation. The generation number of the copy will be reset to 0. If you use \verb?aevol_propagate? repeatedly 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).
\subsection*{Options}
\begin{verbatim}
-h, --help
print this 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_propagate repeatedly to initialize
several simulations, you should specify a different 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 expression.
-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.
\end{verbatim}
\newpage
\section{aevol\_modify}
\label{sec:aevol-modify}
\subsection*{Synopsis}
\begin{verbatim}
aevol_modify -h or --help
aevol_modify -V or --version
aevol_modify -g GENER [-f param_file]
\end{verbatim}
\subsection*{Description}
Modify an experiment as specified in param\_file.
\subsection*{Options}
\begin{verbatim}
-h, --help
print this help, then exit
-V, --version
print version number, then exit
-g, --gener GENER
specify generation number
-f, --file param_file
specify parameter file (default: param.in)
\end{verbatim}
\clearemptydoublepage
|
