scrm simulates the evolution of genetic sequences. It takes a neutral evolutionary model as input, and generates random sequences that evolved under the model. As coalescent simulator, it traces the ancestry of the sampled sequences backwards in time and is therefore extremely efficient. Compared to other coalescent simulators, it can simulate chromosome-scale sequences without a measureable reduction of genetic linkage between different sites.
Stable Release (recommended)
Development Version From GitHub
You can also install
scrm directly from the git repository. Here, you need to install
On Debian/Ubuntu based systems:
apt-get install build-essential autoconf autoconf-archive libcppunit-dev
On Mac OS:
port install automake autoconf autoconf-archive cppunit
Afterwards you can build the binary using
We designed scrm to be compatible to the famous program
ms from Richard R. Hudson.
You can use it as a drop in replacement for
ms if you avoid the options
Details are available in the wiki.
If you encounter problems while using scrm, please
file a bug report or mail to
develop (at) paulstaab.de.
scrm is described in the manuscript
Paul R. Staab, Sha Zhu, Dirk Metzler and Gerton Lunter. scrm: efficiently simulating long sequences using the approximated coalescent with recombination. Bioinformatics (2015) 31 (10): 1680-1682. doi:10.1093/bioinformatics/btu861.
You can freely use all code in this project under the conditions of the GNU GPL Version 3 or later.