pcrcoal is an R package implementing the coalescent approach to PCR simulation developed by Weiss and von Haeseler (NAR, 1997). The package reports the simulated genealogies as phylo objects compatible with the ape package. The reported branch lengths are equal to the number of replications that occured in the respective lineage.

The package source can be found at GitHub.

References

Weiss, G, von Haeseler, A (1997) A coalescent approach to the polymerase chain reaction. NAR 25(15): 3082-3087 http://dx.doi.org/10.1093/nar/25.15.3082

Sipos, B, Massingham, T, Stütz, AM, Goldman, N (2012) An Improved Protocol for Sequencing of Repetitive Genomic Regions and Structural Variations Using Mutagenesis and Next Generation Sequencing. PLoS ONE 7(8): e43359 https://doi.org/10.1371/journal.pone.0043359

Installation

The most practical way to install the package is using the devtools package:

library(devtools)
install_github("botond-sipos/pcrcoal")

Usage

An example of how to use the package can be found at GitHub.