| layout | title | tagline | version |
|---|---|---|---|
page |
Next-Gen Coalescent Simulation |
1.7.4 |
{% include JB/setup %}
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.
{% for post in site.posts limit:5 %}
- {{ post.date | date_to_string }}: [{{ post.title }}]({{ site.url }}{{ post.url }}) {% endfor %}
- Source: [scrm v{{ page.version }}](https://github.com/scrm/scrm/releases/download/v{{ page.version }}/scrm-src.tar.gz).
- 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,
scrmis available viaapt-get install scrm. There are also packages for Fedora, openSUSE, CentOS, RHEL, Scientific Linux. We also provide [statically linked x64 binaries](https://github.com/scrm/scrm/releases/download/v{{ page.version }}/scrm-x64-static.tar.gz). - Windows Binaries:
[64 Bit (recommended)](https://github.com/scrm/scrm/releases/download/v{{ page.version }}/scrm-win64.zip) and
[32 Bit](https://github.com/scrm/scrm/releases/download/v{{ page.version }}/scrm-win32.zip).
Due to a problem with gcc, scrm fails to select a random seed if none is given
via the
-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.
