Simulating the Evolution of Biological Sequences

A coalescent simulator that allows the rapid simulation of biological sequences under neutral models of evolution, see Staab et al. (2015) . 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 R Package

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.

Installation

It is recommended to use the current CRAN version. It can be installed from within R using

install.packages('scrm')

Usage

Use the function scrm::scrm() to call scrm:

library('scrm')
sum_stats <- scrm('5 1 -r 10 100 -t 5 -oSFS')

Help & Documentation

• The basic usage of scrm::scrm() is explained in its R help page help('scrm').
• The package contains a vignette on scrm's command line arguments: vignette('scrm-Arguments').
• Online documentation for the command line program is available in scrm's Wiki.

Citation

Please cite the following article when using scrm in a 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.

Bug Reports

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.