simulator_msms

activate_msms

This adds the simulator 'msms' to the list of available simulators. To add
msms, you need to download the jar file and have Java installed on your
system.

Coalescent simulators can rapidly simulate biological sequences
evolving according to a given model of evolution.
You can use this package to specify such models, to conduct the simulations
and to calculate additional statistics from the results (Staab, Metzler,
2016 <doi:10.1093/bioinformatics/btw098>).
It relies on existing simulators for doing the simulation, and currently
supports the programs 'ms', 'msms' and 'scrm'. It also supports finite-sites
mutation models by combining the simulators with the program 'seq-gen'.
Coala provides functions for calculating certain summary statistics, which
can also be applied to actual biological data.
One possibility to import data is through the 'PopGenome' package
(<https://github.com/pievos101/PopGenome>).

Dirk Metzler

coala

A Framework for Coalescent Simulation

Paul Staab

Jorge E. Amaya Romero

simulator_msms function

<dl><dt>jar</dt>
<dd>The path of the msms jar file.</dd>
<dt>java</dt>
<dd>The path of the java executable on your system.</dd>
<dt>priority</dt>
<dd>The priority for this simulator. If multiple simulators
can simulate a model, the one with the highest priority will be used.</dd>
<dt>download</dt>
<dd>If set to <code>TRUE</code>, coala will try to download
the msms jar file. In that case, the <code>jar</code> argument
is not required.</dd></dl>

Arguments

Simulator: msms — simulator_msms

<dl>

<dt>jar</dt>
<dd>The path of the msms jar file.</dd>


<dt>java</dt>
<dd>The path of the java executable on your system.</dd>


<dt>priority</dt>
<dd>The priority for this simulator. If multiple simulators
can simulate a model, the one with the highest priority will be used.</dd>


<dt>download</dt>
<dd>If set to <code>TRUE</code>, coala will try to download
the msms jar file. In that case, the <code>jar</code> argument
is not required.</dd>

</dl>

simulator_msms: Simulator: msms

Description

Usage

Arguments

References

See Also

Examples