scrm

Simulating the Evolution of Biological Sequences

Zhu Sha, Gerton Lunter, Paul R. Staab, Dirk Metzler

Last update: 8 January 2024

Copyright license: GNU General Public License

Software version identifier: 1.7.4-0, 1.3-1, 1.3-2, 1.3-3, 1.5.0-1, 1.6.0-2, 1.7.2-0, 1.7.2-1, 1.7.2-3, 1.7.2-4, 1.7.3-1, 1.7.5

Source code repository: https://github.com/cran/scrm

Description

A coalescent simulator that allows the rapid simulation of biological sequences under neutral models of evolution, see Staab et al. (2015) <doi:10.1093/bioinformatics/btu861>. 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.

Cites work

scrm: efficiently simulating long sequences using the approximated coalescent with recombination