Examples modified by Victor Spirin

Victor Spirin — Tue, 07 Jan 2014 18:50:10 -0000

Discussion for Examples page

Victor Spirin — Tue, 07 Jan 2014 18:37:06 -0000

Selection and Dominance

The user can specify selection coefficient s and dominance h
parameters. The fitness of heterozygotes is $1+hs$ ($h=0$ for recessive, 0.5
for codominant and 1 for dominant). Values below 0 and above 1 are for
underdominance and overdominance. Default value of $h$ is set to 0.5.
The fitness of homozygotes is $1+s$.

To set dominance parameter to 0.75, for example, add
\verb|--dominance 0.75|
\begin{verbatim}
FS -N P 1 10000 -N P 2 10000 -B 1.0 -TS 0.002 -TW 0.002 -TE 0.01
-t 4e-4 -r 4e-4 -L 100000 -s 159 --selectionCoeff 1000
--selectionStartSite 49700 --selectionEndSite 50300
-n 1000 1000 --outputTime 0.001 0.0025 0.005 0.0075 -o ssw21
-Tg P 2 0.00 0.01 P 1 0.00 0.01 --dominance 0.75
\end{verbatim}

Specifying \verb|--selectionStartSite| and \verb|--selectionEndSite|
is essential. If the selection acts on the entire genome, these two
parameters should be set to 0 and \verb|genomeLength| $L$. By default, if
these two parameters are not specified, the selection will act on only
one site. This site will be chosen after \verb|BURNIN| and will be
the closest to $L/2$ polymorphic site. This is the sample command
line to see sweep on one site:
\begin{verbatim}
FS -N P 1 10000 -N P 2 10000 -B 1.0 -TS 0.002 -TW 0.002 -TE 0.01
-t 4e-4 -r 4e-4 -L 100000 -s 159 --selectionCoeff 1000
-n 1000 1000 --outputTime 0.001 0.0025 0.005 0.0075 -o ssw21
-Tg P 2 0.00 0.01 P 1 0.00 0.01 --dominance 0.75
\end{verbatim}

\subsection{Population Expansion}
\begin{verbatim}
FS -N P 1 10000 -N P 2 10000 -B 1.0 -TS 0.002 -TW 0.002 -TE 0.01
-t 4e-4 -r 4e-4 -L 100000 -s 159 --selectionCoeff 1000
--selectionStartSite 49700 --selectionEndSite 50300 --fitnessBoolOR
-n 1000 1000 --outputTime 0.001 0.0025 0.005 0.0075 -o ssw21
-Tg P 2 0.00 0.01 P 1 0.00 0.01
\end{verbatim}

The expansion part is \verb|-Tg P 1 0.00 0.01 P 2 0.00 0.01|. Six arguments after \verb|-Tg| are mandatory. P1 starts expanding at 0.00 after BURNIN and expands at a rate 1.01 every generation (0.01 corresponds to this 1\% growth). Same with P2.

Examples modified by Victor Spirin

Victor Spirin — Sun, 05 Jan 2014 23:03:05 -0000

Recent changes to Examples

Examples modified by Victor Spirin

Discussion for Examples page

Selection and Dominance

Examples modified by Victor Spirin

Selection and dominance

Population expansion