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.

News

• 07 Mar 2020: Version 1.7.4 Released
• 18 Nov 2018: Version 1.7.3 Released
• 10 Apr 2016: Version 1.7.2 Released
• 23 Mar 2016: Version 1.7.1 Released
• 07 Feb 2016: Version 1.7.0 Released

Downloads

• Source: scrm v1.7.4.
• 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 and Debian 8, scrm is available via apt-get install scrm. There are also packages for Fedora, openSUSE, CentOS, RHEL, Scientific Linux. We also provide statically linked x64 binaries.
• Windows Binaries: 64 Bit (recommended) and 32 Bit. Due to a problem with gcc, scrm fails to select a random seed if none is given via the -seed argument. Consequently, you should always use the -seed argument 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/scrm to build the latest version.
• Using Bioconda: Use conda install scrm.

Publication

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.

Documentation

Please refer to scrm’s wiki for instructions on how to compile or use scrm.

Links

• scrm’s GitHub site
• scrm’s wiki
• Bugtracker