simulator_ms

activate_ms

This function adds the simulator 'ms' to the list of available simulators.
In order to use 'ms', you need to install the CRAN package phyclust.
By default, 'scrm' will be preferred over 'ms'. Raise the priority of 'ms'
to change this behavior.

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_ms function

<dl><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></dl>

Arguments

Simulator: ms — simulator_ms

<dl>

<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>

</dl>

simulator_ms: Simulator: ms

Description

Usage

Arguments

References

See Also

Examples