A coalescent simulator that allows the rapid simulation of biological sequences under neutral models of evolution. Different to other coalescent based simulations, it has an optional approximation parameter that allows for high accuracy while maintaining a linear run time cost for long sequences. It is optimized for simulating massive data sets as produced by Next- Generation Sequencing technologies for up to several thousand sequences.
scrm is a coalescence simulator for the evolution of biological sequences. It is available as a command line program at scrm.github.io.
This R package contains a copy scrm, packaged for convenient usage in R.
It is recommended to use the current CRAN version. It can be installed from within R using
The development version can be installed from GitHub using
Use the function
scrm::scrm() to call scrm:
library('scrm')sum_stats <- scrm('5 1 -r 10 100 -t 5 -oSFS')
scrm::scrm()is explained in its R help page
Please cite the following article when using scrm in a publication:
scrm: efficiently simulating long sequences using the approximated coalescent with recombination. Bioinformatics (2015) 31 (10): 1680-1682. doi:10.1093/bioinformatics/btu861.
Please report any problems via the issue tracker
or via email to
develop (at) paulstaab (dot) de.
Please include the version you are using and the exact command that causes the problem including seed (if applicable) in the report. Also, feel free to suggest features there.
testthatis not available (#25).