scrm is a coalescent simulator for biological sequences. Different to similar programs, it can approximate the Ancestral Recombination Graph as closely as needed, but still has only linear runtime cost for long sequences. It allows you to rapidly simulate chromosome scale sequences with essentially correct genetic linkage.
- 10 Apr 2016: Version 1.7.2 Released
- 23 Mar 2016: Version 1.7.1 Released
- 07 Feb 2016: Version 1.7.0 Released
- 09 Jul 2015: Version 1.6.1 Released
- 04 Jun 2015: Version 1.6.0 Released
- Source: scrm v1.7.2.
- R: scrm is available as R package on CRAN
for all major platforms. Use
install.packages('scrm')in R to install it.
- Linux: Starting from Ubuntu 16.04,
scrmis available via
apt-get install scrm. There are also Packages for Debian, Fedora, openSUSE, CentOS, RHEL, Scientific Linux. We also provide statically linked x64 binaries.
- Windows Binaries:
64 Bit (recommended) and
Due to a problem with gcc, scrm fails to select a random seed if none is given
-seedargument. Consequently, you should always use the
-seedargument when using the windows binaries. Alternatively, consider using the R package.
- Mac: scrm is available via the Homebrew package manager. After installing Homebrew, run
brew install homebrew/science/scrmto build the latest version.
- Using Bioconda: Use
conda install scrm.
If you use scrm in a publication, please cite the following publication:
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.
Please refer to scrm’s wiki for instructions on how to compile or use scrm.